From 717eb19aeb012ee7141b962a4d8e10d838324320 Mon Sep 17 00:00:00 2001
From: = <=>
Date: Thu, 27 Jun 2024 07:36:36 +0200
Subject: [PATCH 01/23] wip: chore: restructure query schema type (keeping
 format)

---
 src/seqvars/query/interpreter/clinvar.rs   |  16 +--
 src/seqvars/query/interpreter/frequency.rs |  83 +++++++-----
 src/seqvars/query/schema.rs                | 141 ++++++++++++---------
 3 files changed, 138 insertions(+), 102 deletions(-)

diff --git a/src/seqvars/query/interpreter/clinvar.rs b/src/seqvars/query/interpreter/clinvar.rs
index 3971dac4..587de6b8 100644
--- a/src/seqvars/query/interpreter/clinvar.rs
+++ b/src/seqvars/query/interpreter/clinvar.rs
@@ -41,19 +41,19 @@ pub fn passes(
             .unwrap_or_default();
 
         let result = match description.to_lowercase().as_str() {
-            "benign" => query.clinvar_include_benign,
+            "benign" => query.clinvar.include_benign,
             "benign/likely benign" => {
-                query.clinvar_include_benign || query.clinvar_include_likely_benign
+                query.clinvar.include_benign || query.clinvar.include_likely_benign
             }
-            "likely benign" => query.clinvar_include_likely_benign,
-            "pathogenic" => query.clinvar_include_pathogenic,
+            "likely benign" => query.clinvar.include_likely_benign,
+            "pathogenic" => query.clinvar.include_pathogenic,
             "pathogenic/likely pathogenic" => {
-                query.clinvar_include_pathogenic || query.clinvar_include_likely_pathogenic
+                query.clinvar.include_pathogenic || query.clinvar.include_likely_pathogenic
             }
-            "likely pathogenic" => query.clinvar_include_likely_pathogenic,
-            "uncertain significance" => query.clinvar_include_uncertain_significance,
+            "likely pathogenic" => query.clinvar.include_likely_pathogenic,
+            "uncertain significance" => query.clinvar.include_uncertain_significance,
             "conflicting classifications of pathogenicity" => {
-                query.clinvar_include_uncertain_significance
+                query.clinvar.include_uncertain_significance
             }
             _ => {
                 // We could also downtone this to debug.
diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs
index 09b0936c..da762480 100644
--- a/src/seqvars/query/interpreter/frequency.rs
+++ b/src/seqvars/query/interpreter/frequency.rs
@@ -17,39 +17,39 @@ pub fn passes(query: &CaseQuery, s: &SequenceVariant) -> Result<bool, anyhow::Er
             tracing::trace!("variant {:?} fails HelixMtDb frequency filter {:?}", s, &q);
             return Ok(false);
         }
-    } else if q.gnomad_exomes_enabled
-        && (q.gnomad_exomes_frequency.is_some()
-            && s.gnomad_exomes_af() > q.gnomad_exomes_frequency.expect("tested before")
-            || q.gnomad_exomes_heterozygous.is_some()
-                && s.gnomad_exomes_het > q.gnomad_exomes_heterozygous.expect("tested before")
-            || q.gnomad_exomes_homozygous.is_some()
-                && s.gnomad_exomes_hom > q.gnomad_exomes_homozygous.expect("tested before")
-            || q.gnomad_exomes_hemizygous.is_some()
-                && s.gnomad_exomes_hemi > q.gnomad_exomes_hemizygous.expect("tested before"))
+    } else if q.gnomad.exomes_enabled
+        && (q.gnomad.exomes_frequency.is_some()
+            && s.gnomad_exomes_af() > q.gnomad.exomes_frequency.expect("tested before")
+            || q.gnomad.exomes_heterozygous.is_some()
+                && s.gnomad_exomes_het > q.gnomad.exomes_heterozygous.expect("tested before")
+            || q.gnomad.exomes_homozygous.is_some()
+                && s.gnomad_exomes_hom > q.gnomad.exomes_homozygous.expect("tested before")
+            || q.gnomad.exomes_hemizygous.is_some()
+                && s.gnomad_exomes_hemi > q.gnomad.exomes_hemizygous.expect("tested before"))
     {
         tracing::trace!(
             "variant {:?} fails gnomAD exomes frequency filter {:?}",
             s,
-            &q.gnomad_exomes_frequency
+            &q.gnomad.exomes_frequency
         );
         return Ok(false);
     }
 
-    if q.gnomad_genomes_enabled
-        && (q.gnomad_genomes_frequency.is_some()
-            && s.gnomad_genomes_af() > q.gnomad_genomes_frequency.expect("tested before")
-            || q.gnomad_genomes_heterozygous.is_some()
-                && s.gnomad_genomes_het > q.gnomad_genomes_heterozygous.expect("tested before")
-            || q.gnomad_genomes_homozygous.is_some()
-                && s.gnomad_genomes_hom > q.gnomad_genomes_homozygous.expect("tested before")
+    if q.gnomad.genomes_enabled
+        && (q.gnomad.genomes_frequency.is_some()
+            && s.gnomad_genomes_af() > q.gnomad.genomes_frequency.expect("tested before")
+            || q.gnomad.genomes_heterozygous.is_some()
+                && s.gnomad_genomes_het > q.gnomad.genomes_heterozygous.expect("tested before")
+            || q.gnomad.genomes_homozygous.is_some()
+                && s.gnomad_genomes_hom > q.gnomad.genomes_homozygous.expect("tested before")
             || !is_mtdna
-                && q.gnomad_genomes_hemizygous.is_some()
-                && s.gnomad_genomes_hemi > q.gnomad_genomes_hemizygous.expect("tested before"))
+                && q.gnomad.genomes_hemizygous.is_some()
+                && s.gnomad_genomes_hemi > q.gnomad.genomes_hemizygous.expect("tested before"))
     {
         tracing::trace!(
             "variant {:?} fails gnomAD genomes frequency filter {:?}",
             s,
-            &q.gnomad_genomes_frequency
+            &q.gnomad.genomes_frequency
         );
         return Ok(false);
     }
@@ -130,12 +130,17 @@ mod test {
         #[case] query_gnomad_exomes_hemizygous: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
+        use crate::seqvars::query::schema::GnomadOptions;
+
         let query = CaseQuery {
-            gnomad_exomes_enabled: query_gnomad_exomes_enabled,
-            gnomad_exomes_frequency: query_gnomad_exomes_frequency,
-            gnomad_exomes_heterozygous: query_gnomad_exomes_heterozygous,
-            gnomad_exomes_homozygous: query_gnomad_exomes_homozygous,
-            gnomad_exomes_hemizygous: query_gnomad_exomes_hemizygous,
+            gnomad: GnomadOptions {
+                exomes_enabled: query_gnomad_exomes_enabled,
+                exomes_frequency: query_gnomad_exomes_frequency,
+                exomes_heterozygous: query_gnomad_exomes_heterozygous,
+                exomes_homozygous: query_gnomad_exomes_homozygous,
+                exomes_hemizygous: query_gnomad_exomes_hemizygous,
+                ..Default::default()
+            },
             ..Default::default()
         };
         let seq_var = SequenceVariant {
@@ -241,12 +246,17 @@ mod test {
         #[case] query_gnomad_genomes_hemizygous: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
+        use crate::seqvars::query::schema::GnomadOptions;
+
         let query = CaseQuery {
-            gnomad_genomes_enabled: query_gnomad_genomes_enabled,
-            gnomad_genomes_frequency: query_gnomad_genomes_frequency,
-            gnomad_genomes_heterozygous: query_gnomad_genomes_heterozygous,
-            gnomad_genomes_homozygous: query_gnomad_genomes_homozygous,
-            gnomad_genomes_hemizygous: query_gnomad_genomes_hemizygous,
+            gnomad: GnomadOptions {
+                genomes_enabled: query_gnomad_genomes_enabled,
+                genomes_frequency: query_gnomad_genomes_frequency,
+                genomes_heterozygous: query_gnomad_genomes_heterozygous,
+                genomes_homozygous: query_gnomad_genomes_homozygous,
+                genomes_hemizygous: query_gnomad_genomes_hemizygous,
+                ..Default::default()
+            },
             ..Default::default()
         };
         let seq_var = SequenceVariant {
@@ -424,11 +434,16 @@ mod test {
         #[case] query_gnomad_genomes_homoplasmic: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
+        use crate::seqvars::query::schema::GnomadOptions;
+
         let query = CaseQuery {
-            gnomad_genomes_enabled: query_gnomad_genomes_enabled,
-            gnomad_genomes_frequency: query_gnomad_genomes_frequency,
-            gnomad_genomes_heterozygous: query_gnomad_genomes_heteroplasmic,
-            gnomad_genomes_homozygous: query_gnomad_genomes_homoplasmic,
+            gnomad: GnomadOptions {
+                genomes_enabled: query_gnomad_genomes_enabled,
+                genomes_frequency: query_gnomad_genomes_frequency,
+                genomes_heterozygous: query_gnomad_genomes_heteroplasmic,
+                genomes_homozygous: query_gnomad_genomes_homoplasmic,
+                ..Default::default()
+            },
             ..Default::default()
         };
         let seq_var = SequenceVariant {
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 12b932c3..36c1ccc0 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -150,6 +150,52 @@ pub struct GenomicRegion {
     pub range: Option<Range>,
 }
 
+serde_with::with_prefix!(prefix_clinvar "clinvar_");
+#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
+#[serde(default)]
+pub struct ClinVarOptions {
+    /// Whether to include benign ClinVar variants.
+    pub include_benign: bool,
+    /// Whether to include pathogenic ClinVar variants.
+    pub include_pathogenic: bool,
+    /// Whether to include likely benign ClinVar variants.
+    pub include_likely_benign: bool,
+    /// Whether to include likely pathogenic ClinVar variants.
+    pub include_likely_pathogenic: bool,
+    /// Whether to include uncertain significance ClinVar variants.
+    pub include_uncertain_significance: bool,
+    /// Whether to include conflicting interpretation ClinVar variants.
+    pub include_conflicting_classifications: bool,
+}
+
+serde_with::with_prefix!(prefix_gnomad "gnomad_");
+#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
+#[serde(default)]
+pub struct GnomadOptions {
+    /// Whether to enable filtration by gnomAD exomes.
+    pub exomes_enabled: bool,
+    /// Whether to enable filtration by gnomAD genomes
+    pub genomes_enabled: bool,
+
+    /// Maximal frequency in gnomAD exomes.
+    pub exomes_frequency: Option<f32>,
+    /// Maximal number of heterozygous carriers in gnomAD exomes.
+    pub exomes_heterozygous: Option<i32>,
+    /// Maximal number of homozygous carriers in gnomAD exomes.
+    pub exomes_homozygous: Option<i32>,
+    /// Maximal number of hemizygous carriers in gnomAD exomes.
+    pub exomes_hemizygous: Option<i32>,
+
+    /// Maximal frequency in gnomAD genomes.
+    pub genomes_frequency: Option<f32>,
+    /// Maximal number of heterozygous carriers in gnomAD genomes.
+    pub genomes_heterozygous: Option<i32>,
+    /// Maximal number of homozygous carriers in gnomAD genomes.
+    pub genomes_homozygous: Option<i32>,
+    /// Maximal number of hemizygous carriers in gnomAD genomes.
+    pub genomes_hemizygous: Option<i32>,
+}
+
 /// Data structure with a single query.
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -185,46 +231,18 @@ pub struct CaseQuery {
 
     /// Wether to require ClinVar membership.
     pub require_in_clinvar: bool,
-    /// Whether to include benign ClinVar variants.
-    pub clinvar_include_benign: bool,
-    /// Whether to include pathogenic ClinVar variants.
-    pub clinvar_include_pathogenic: bool,
-    /// Whether to include likely benign ClinVar variants.
-    pub clinvar_include_likely_benign: bool,
-    /// Whether to include likely pathogenic ClinVar variants.
-    pub clinvar_include_likely_pathogenic: bool,
-    /// Whether to include uncertain significance ClinVar variants.
-    pub clinvar_include_uncertain_significance: bool,
-    /// Whether to include conflicting interpretation ClinVar variants.
-    pub clinvar_include_conflicting_classifications: bool,
 
-    /// Whether to enable filtration by gnomAD exomes.
-    pub gnomad_exomes_enabled: bool,
-    /// Whether to enable filtration by gnomAD genomes
-    pub gnomad_genomes_enabled: bool,
+    #[serde(flatten, with = "prefix_clinvar")]
+    pub clinvar: ClinVarOptions,
+
+    #[serde(flatten, with = "prefix_gnomad")]
+    pub gnomad: GnomadOptions,
+
     /// Whether to enable filtration by 1000 Genomes.
     pub inhouse_enabled: bool,
     /// Whether to enable filtration by mtDB.
     pub helixmtdb_enabled: bool,
 
-    /// Maximal frequency in gnomAD exomes.
-    pub gnomad_exomes_frequency: Option<f32>,
-    /// Maximal number of heterozygous carriers in gnomAD exomes.
-    pub gnomad_exomes_heterozygous: Option<i32>,
-    /// Maximal number of homozygous carriers in gnomAD exomes.
-    pub gnomad_exomes_homozygous: Option<i32>,
-    /// Maximal number of hemizygous carriers in gnomAD exomes.
-    pub gnomad_exomes_hemizygous: Option<i32>,
-
-    /// Maximal frequency in gnomAD genomes.
-    pub gnomad_genomes_frequency: Option<f32>,
-    /// Maximal number of heterozygous carriers in gnomAD genomes.
-    pub gnomad_genomes_heterozygous: Option<i32>,
-    /// Maximal number of homozygous carriers in gnomAD genomes.
-    pub gnomad_genomes_homozygous: Option<i32>,
-    /// Maximal number of hemizygous carriers in gnomAD genomes.
-    pub gnomad_genomes_hemizygous: Option<i32>,
-
     /// Maximal number of in-house carriers.
     pub inhouse_carriers: Option<i32>,
     /// Maximal number of in-house heterozygous carriers.
@@ -242,13 +260,24 @@ pub struct CaseQuery {
     pub helixmtdb_homoplasmic: Option<i32>,
 }
 
+impl Default for ClinVarOptions {
+    fn default() -> Self {
+        Self {
+            include_benign: true,
+            include_pathogenic: true,
+            include_likely_benign: true,
+            include_likely_pathogenic: true,
+            include_uncertain_significance: true,
+            include_conflicting_classifications: true,
+        }
+    }
+}
+
 impl Default for CaseQuery {
     /// Returns default values for a `CaseQuery` which makes all variants pass.
     fn default() -> Self {
         Self {
             consequences: mehari::annotate::seqvars::ann::Consequence::all(),
-            gnomad_exomes_enabled: Default::default(),
-            gnomad_genomes_enabled: Default::default(),
             inhouse_enabled: Default::default(),
             helixmtdb_enabled: Default::default(),
             quality: Default::default(),
@@ -262,20 +291,8 @@ impl Default for CaseQuery {
             gene_allowlist: Default::default(),
             genomic_regions: Default::default(),
             require_in_clinvar: Default::default(),
-            clinvar_include_benign: true,
-            clinvar_include_pathogenic: true,
-            clinvar_include_likely_benign: true,
-            clinvar_include_likely_pathogenic: true,
-            clinvar_include_uncertain_significance: true,
-            clinvar_include_conflicting_classifications: true,
-            gnomad_exomes_frequency: Default::default(),
-            gnomad_exomes_heterozygous: Default::default(),
-            gnomad_exomes_homozygous: Default::default(),
-            gnomad_exomes_hemizygous: Default::default(),
-            gnomad_genomes_frequency: Default::default(),
-            gnomad_genomes_heterozygous: Default::default(),
-            gnomad_genomes_homozygous: Default::default(),
-            gnomad_genomes_hemizygous: Default::default(),
+            clinvar: Default::default(),
+            gnomad: Default::default(),
             inhouse_carriers: Default::default(),
             inhouse_heterozygous: Default::default(),
             inhouse_homozygous: Default::default(),
@@ -293,23 +310,27 @@ impl CaseQuery {
         self.genotype.values().any(|gt_choice| {
             matches!(
                 gt_choice,
-                Some(GenotypeChoice::ComphetIndex)
-                    | Some(GenotypeChoice::RecessiveIndex)
-                    | Some(GenotypeChoice::RecessiveParent)
+                Some(
+                    GenotypeChoice::ComphetIndex
+                        | GenotypeChoice::RecessiveIndex
+                        | GenotypeChoice::RecessiveParent
+                )
             )
         })
     }
 
     /// Returns name of the recessive index sample.
     pub fn index_sample(&self) -> Option<String> {
-        self.genotype
-            .iter()
-            .find_map(|(name, gt_choice)| match gt_choice {
-                Some(GenotypeChoice::ComphetIndex) | Some(GenotypeChoice::RecessiveIndex) => {
-                    Some(name.clone())
+        for (name, gt_choice) in &self.genotype {
+            match gt_choice {
+                Some(GenotypeChoice::ComphetIndex | GenotypeChoice::RecessiveIndex) => {
+                    return Some(name.clone())
                 }
-                _ => None,
-            })
+                _ => continue,
+            }
+        }
+
+        None
     }
 }
 /// Information on the call as written out by ingest.

From ded525ba34e65958d2643378e64a5fcdfedecee8 Mon Sep 17 00:00:00 2001
From: = <=>
Date: Thu, 27 Jun 2024 08:21:24 +0200
Subject: [PATCH 02/23] chore: wip: more restructuring

---
 src/seqvars/query/interpreter/frequency.rs    | 26 ++++---
 src/seqvars/query/schema.rs                   | 77 +++++++++++--------
 ...ema__test__smoke_test_load@empty.json.snap |  4 +-
 ...hema__test__smoke_test_load@full.json.snap |  4 +-
 ...test__smoke_test_load@with_extra.json.snap |  4 +-
 5 files changed, 66 insertions(+), 49 deletions(-)

diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs
index da762480..eb6e81ce 100644
--- a/src/seqvars/query/interpreter/frequency.rs
+++ b/src/seqvars/query/interpreter/frequency.rs
@@ -6,13 +6,13 @@ pub fn passes(query: &CaseQuery, s: &SequenceVariant) -> Result<bool, anyhow::Er
     let is_mtdna = annonars::common::cli::canonicalize(&s.chrom) == "MT";
 
     if is_mtdna {
-        if q.helixmtdb_enabled
-            && (q.helixmtdb_frequency.is_some()
-                && s.helixmtdb_af() > q.helixmtdb_frequency.expect("tested before")
-                || q.helixmtdb_heteroplasmic.is_some()
-                    && s.helix_het > q.helixmtdb_heteroplasmic.expect("tested before")
-                || q.helixmtdb_homoplasmic.is_some()
-                    && s.helix_hom > q.helixmtdb_homoplasmic.expect("tested before"))
+        if q.helixmtdb.enabled
+            && (q.helixmtdb.frequency.is_some()
+                && s.helixmtdb_af() > q.helixmtdb.frequency.expect("tested before")
+                || q.helixmtdb.heteroplasmic.is_some()
+                    && s.helix_het > q.helixmtdb.heteroplasmic.expect("tested before")
+                || q.helixmtdb.homoplasmic.is_some()
+                    && s.helix_hom > q.helixmtdb.homoplasmic.expect("tested before"))
         {
             tracing::trace!("variant {:?} fails HelixMtDb frequency filter {:?}", s, &q);
             return Ok(false);
@@ -343,11 +343,15 @@ mod test {
         #[case] query_helix_homoplasmic: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
+        use crate::seqvars::query::schema::HelixMtDbOptions;
+
         let query = CaseQuery {
-            helixmtdb_enabled: query_helix_enabled,
-            helixmtdb_frequency: query_helix_frequency,
-            helixmtdb_heteroplasmic: query_helix_heteroplasmic,
-            helixmtdb_homoplasmic: query_helix_homoplasmic,
+            helixmtdb: HelixMtDbOptions {
+                enabled: query_helix_enabled,
+                frequency: query_helix_frequency,
+                heteroplasmic: query_helix_heteroplasmic,
+                homoplasmic: query_helix_homoplasmic,
+            },
             ..Default::default()
         };
         let seq_var = SequenceVariant {
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 36c1ccc0..d7034f74 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -196,6 +196,40 @@ pub struct GnomadOptions {
     pub genomes_hemizygous: Option<i32>,
 }
 
+serde_with::with_prefix!(prefix_inhouse "inhouse_");
+#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
+#[serde(default)]
+/// TODO: currently unused?
+pub struct InhouseOptions {
+    /// Whether to enable filtration by 1000 Genomes.
+    pub enabled: bool,
+    /// Maximal number of in-house carriers.
+    pub carriers: Option<i32>,
+    /// Maximal number of in-house heterozygous carriers.
+    pub heterozygous: Option<i32>,
+    /// Maximal number of in-house homozygous carriers.
+    pub homozygous: Option<i32>,
+    /// Maximal number of in-house hemizygous carriers.
+    pub hemizygous: Option<i32>,
+}
+
+serde_with::with_prefix!(prefix_helixmtdb "helixmtdb_");
+#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
+#[serde(default)]
+/// TODO: currently unused?
+pub struct HelixMtDbOptions {
+    /// Whether to enable filtration by mtDB.
+    pub enabled: bool,
+    /// Maximal frequency in HelixMtDb
+    pub frequency: Option<f32>,
+    /// Maximal number of heterozygous carriers in HelixMtDb.
+    pub heteroplasmic: Option<i32>,
+    /// Maximal number of homozygous carriers in HelixMtDb.
+    pub homoplasmic: Option<i32>,
+}
+
+
+
 /// Data structure with a single query.
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -229,35 +263,21 @@ pub struct CaseQuery {
     /// List of genomic regions to limit restrict the resulting variants to.
     pub genomic_regions: Option<Vec<GenomicRegion>>,
 
+    /// TODO: wanted schema is defined in issue, emily reading comprehension 10/10
+
     /// Wether to require ClinVar membership.
     pub require_in_clinvar: bool,
-
+    /// ClinVar related filter options.
     #[serde(flatten, with = "prefix_clinvar")]
     pub clinvar: ClinVarOptions,
-
+    /// GnomAD related filter options.
     #[serde(flatten, with = "prefix_gnomad")]
     pub gnomad: GnomadOptions,
-
-    /// Whether to enable filtration by 1000 Genomes.
-    pub inhouse_enabled: bool,
-    /// Whether to enable filtration by mtDB.
-    pub helixmtdb_enabled: bool,
-
-    /// Maximal number of in-house carriers.
-    pub inhouse_carriers: Option<i32>,
-    /// Maximal number of in-house heterozygous carriers.
-    pub inhouse_heterozygous: Option<i32>,
-    /// Maximal number of in-house homozygous carriers.
-    pub inhouse_homozygous: Option<i32>,
-    /// Maximal number of in-house hemizygous carriers.
-    pub inhouse_hemizygous: Option<i32>,
-
-    /// Maximal frequency in HelixMtDb
-    pub helixmtdb_frequency: Option<f32>,
-    /// Maximal number of heterozygous carriers in HelixMtDb.
-    pub helixmtdb_heteroplasmic: Option<i32>,
-    /// Maximal number of homozygous carriers in HelixMtDb.
-    pub helixmtdb_homoplasmic: Option<i32>,
+    /// Inhouse related filter options. TODO BETTER COMMENT
+    #[serde(flatten, with = "prefix_inhouse")]
+    pub inhouse: InhouseOptions,
+    #[serde(flatten, with = "prefix_helixmtdb")]
+    pub helixmtdb: HelixMtDbOptions,
 }
 
 impl Default for ClinVarOptions {
@@ -278,8 +298,7 @@ impl Default for CaseQuery {
     fn default() -> Self {
         Self {
             consequences: mehari::annotate::seqvars::ann::Consequence::all(),
-            inhouse_enabled: Default::default(),
-            helixmtdb_enabled: Default::default(),
+            helixmtdb: Default::default(),
             quality: Default::default(),
             genotype: Default::default(),
             transcripts_coding: true,
@@ -293,13 +312,7 @@ impl Default for CaseQuery {
             require_in_clinvar: Default::default(),
             clinvar: Default::default(),
             gnomad: Default::default(),
-            inhouse_carriers: Default::default(),
-            inhouse_heterozygous: Default::default(),
-            inhouse_homozygous: Default::default(),
-            inhouse_hemizygous: Default::default(),
-            helixmtdb_frequency: Default::default(),
-            helixmtdb_heteroplasmic: Default::default(),
-            helixmtdb_homoplasmic: Default::default(),
+            inhouse: Default::default(),
         }
     }
 }
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
index 12e9ccab..4e61283a 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
@@ -71,8 +71,6 @@ clinvar_include_uncertain_significance: true
 clinvar_include_conflicting_classifications: true
 gnomad_exomes_enabled: false
 gnomad_genomes_enabled: false
-inhouse_enabled: false
-helixmtdb_enabled: false
 gnomad_exomes_frequency: ~
 gnomad_exomes_heterozygous: ~
 gnomad_exomes_homozygous: ~
@@ -81,10 +79,12 @@ gnomad_genomes_frequency: ~
 gnomad_genomes_heterozygous: ~
 gnomad_genomes_homozygous: ~
 gnomad_genomes_hemizygous: ~
+inhouse_enabled: false
 inhouse_carriers: ~
 inhouse_heterozygous: ~
 inhouse_homozygous: ~
 inhouse_hemizygous: ~
+helixmtdb_enabled: false
 helixmtdb_frequency: ~
 helixmtdb_heteroplasmic: ~
 helixmtdb_homoplasmic: ~
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
index 9e20bcc8..4c92ff1f 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
@@ -80,8 +80,6 @@ clinvar_include_uncertain_significance: false
 clinvar_include_conflicting_classifications: true
 gnomad_exomes_enabled: true
 gnomad_genomes_enabled: true
-inhouse_enabled: true
-helixmtdb_enabled: true
 gnomad_exomes_frequency: 0.002
 gnomad_exomes_heterozygous: 20
 gnomad_exomes_homozygous: 0
@@ -90,10 +88,12 @@ gnomad_genomes_frequency: 0.002
 gnomad_genomes_heterozygous: 4
 gnomad_genomes_homozygous: 0
 gnomad_genomes_hemizygous: ~
+inhouse_enabled: true
 inhouse_carriers: 20
 inhouse_heterozygous: ~
 inhouse_homozygous: ~
 inhouse_hemizygous: ~
+helixmtdb_enabled: true
 helixmtdb_frequency: 0.01
 helixmtdb_heteroplasmic: ~
 helixmtdb_homoplasmic: ~
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
index 9e20bcc8..4c92ff1f 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
@@ -80,8 +80,6 @@ clinvar_include_uncertain_significance: false
 clinvar_include_conflicting_classifications: true
 gnomad_exomes_enabled: true
 gnomad_genomes_enabled: true
-inhouse_enabled: true
-helixmtdb_enabled: true
 gnomad_exomes_frequency: 0.002
 gnomad_exomes_heterozygous: 20
 gnomad_exomes_homozygous: 0
@@ -90,10 +88,12 @@ gnomad_genomes_frequency: 0.002
 gnomad_genomes_heterozygous: 4
 gnomad_genomes_homozygous: 0
 gnomad_genomes_hemizygous: ~
+inhouse_enabled: true
 inhouse_carriers: 20
 inhouse_heterozygous: ~
 inhouse_homozygous: ~
 inhouse_hemizygous: ~
+helixmtdb_enabled: true
 helixmtdb_frequency: 0.01
 helixmtdb_heteroplasmic: ~
 helixmtdb_homoplasmic: ~

From bb5bfbcc3a66a3e3a79018d0410fd410c4937075 Mon Sep 17 00:00:00 2001
From: = <=>
Date: Sat, 29 Jun 2024 05:44:15 +0200
Subject: [PATCH 03/23] wip: chore: further restructuring to get closer to
 wanted structure

---
 src/seqvars/query/interpreter/frequency.rs    | 126 ++++++++++--------
 src/seqvars/query/schema.rs                   |  67 ++++++----
 ...ema__test__smoke_test_load@empty.json.snap |  10 +-
 ...hema__test__smoke_test_load@full.json.snap |  10 +-
 ...test__smoke_test_load@with_extra.json.snap |  10 +-
 5 files changed, 125 insertions(+), 98 deletions(-)

diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs
index eb6e81ce..292917ef 100644
--- a/src/seqvars/query/interpreter/frequency.rs
+++ b/src/seqvars/query/interpreter/frequency.rs
@@ -2,54 +2,58 @@ use crate::seqvars::query::schema::{CaseQuery, SequenceVariant};
 
 /// Determine whether the `SequenceVariant` passes the frequency filter.
 pub fn passes(query: &CaseQuery, s: &SequenceVariant) -> Result<bool, anyhow::Error> {
-    let q = &query;
+    let pop = &query.population_freqeuecy;
     let is_mtdna = annonars::common::cli::canonicalize(&s.chrom) == "MT";
 
     if is_mtdna {
-        if q.helixmtdb.enabled
-            && (q.helixmtdb.frequency.is_some()
-                && s.helixmtdb_af() > q.helixmtdb.frequency.expect("tested before")
-                || q.helixmtdb.heteroplasmic.is_some()
-                    && s.helix_het > q.helixmtdb.heteroplasmic.expect("tested before")
-                || q.helixmtdb.homoplasmic.is_some()
-                    && s.helix_hom > q.helixmtdb.homoplasmic.expect("tested before"))
+        if pop.helixmtdb.enabled
+            && (pop.helixmtdb.frequency.is_some()
+                && s.helixmtdb_af() > pop.helixmtdb.frequency.expect("tested before")
+                || pop.helixmtdb.heteroplasmic.is_some()
+                    && s.helix_het > pop.helixmtdb.heteroplasmic.expect("tested before")
+                || pop.helixmtdb.homoplasmic.is_some()
+                    && s.helix_hom > pop.helixmtdb.homoplasmic.expect("tested before"))
         {
-            tracing::trace!("variant {:?} fails HelixMtDb frequency filter {:?}", s, &q);
+            tracing::trace!(
+                "variant {:?} fails HelixMtDb frequency filter {:?}",
+                s,
+                &pop
+            );
             return Ok(false);
         }
-    } else if q.gnomad.exomes_enabled
-        && (q.gnomad.exomes_frequency.is_some()
-            && s.gnomad_exomes_af() > q.gnomad.exomes_frequency.expect("tested before")
-            || q.gnomad.exomes_heterozygous.is_some()
-                && s.gnomad_exomes_het > q.gnomad.exomes_heterozygous.expect("tested before")
-            || q.gnomad.exomes_homozygous.is_some()
-                && s.gnomad_exomes_hom > q.gnomad.exomes_homozygous.expect("tested before")
-            || q.gnomad.exomes_hemizygous.is_some()
-                && s.gnomad_exomes_hemi > q.gnomad.exomes_hemizygous.expect("tested before"))
+    } else if pop.gnomad.exomes_enabled
+        && (pop.gnomad.exomes_frequency.is_some()
+            && s.gnomad_exomes_af() > pop.gnomad.exomes_frequency.expect("tested before")
+            || pop.gnomad.exomes_heterozygous.is_some()
+                && s.gnomad_exomes_het > pop.gnomad.exomes_heterozygous.expect("tested before")
+            || pop.gnomad.exomes_homozygous.is_some()
+                && s.gnomad_exomes_hom > pop.gnomad.exomes_homozygous.expect("tested before")
+            || pop.gnomad.exomes_hemizygous.is_some()
+                && s.gnomad_exomes_hemi > pop.gnomad.exomes_hemizygous.expect("tested before"))
     {
         tracing::trace!(
             "variant {:?} fails gnomAD exomes frequency filter {:?}",
             s,
-            &q.gnomad.exomes_frequency
+            &pop.gnomad.exomes_frequency
         );
         return Ok(false);
     }
 
-    if q.gnomad.genomes_enabled
-        && (q.gnomad.genomes_frequency.is_some()
-            && s.gnomad_genomes_af() > q.gnomad.genomes_frequency.expect("tested before")
-            || q.gnomad.genomes_heterozygous.is_some()
-                && s.gnomad_genomes_het > q.gnomad.genomes_heterozygous.expect("tested before")
-            || q.gnomad.genomes_homozygous.is_some()
-                && s.gnomad_genomes_hom > q.gnomad.genomes_homozygous.expect("tested before")
+    if pop.gnomad.genomes_enabled
+        && (pop.gnomad.genomes_frequency.is_some()
+            && s.gnomad_genomes_af() > pop.gnomad.genomes_frequency.expect("tested before")
+            || pop.gnomad.genomes_heterozygous.is_some()
+                && s.gnomad_genomes_het > pop.gnomad.genomes_heterozygous.expect("tested before")
+            || pop.gnomad.genomes_homozygous.is_some()
+                && s.gnomad_genomes_hom > pop.gnomad.genomes_homozygous.expect("tested before")
             || !is_mtdna
-                && q.gnomad.genomes_hemizygous.is_some()
-                && s.gnomad_genomes_hemi > q.gnomad.genomes_hemizygous.expect("tested before"))
+                && pop.gnomad.genomes_hemizygous.is_some()
+                && s.gnomad_genomes_hemi > pop.gnomad.genomes_hemizygous.expect("tested before"))
     {
         tracing::trace!(
             "variant {:?} fails gnomAD genomes frequency filter {:?}",
             s,
-            &q.gnomad.genomes_frequency
+            &pop.gnomad.genomes_frequency
         );
         return Ok(false);
     }
@@ -130,15 +134,18 @@ mod test {
         #[case] query_gnomad_exomes_hemizygous: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::GnomadOptions;
+        use crate::seqvars::query::schema::{GnomadOptions, PopulationFrequencyOptions};
 
         let query = CaseQuery {
-            gnomad: GnomadOptions {
-                exomes_enabled: query_gnomad_exomes_enabled,
-                exomes_frequency: query_gnomad_exomes_frequency,
-                exomes_heterozygous: query_gnomad_exomes_heterozygous,
-                exomes_homozygous: query_gnomad_exomes_homozygous,
-                exomes_hemizygous: query_gnomad_exomes_hemizygous,
+            population_freqeuecy: PopulationFrequencyOptions {
+                gnomad: GnomadOptions {
+                    exomes_enabled: query_gnomad_exomes_enabled,
+                    exomes_frequency: query_gnomad_exomes_frequency,
+                    exomes_heterozygous: query_gnomad_exomes_heterozygous,
+                    exomes_homozygous: query_gnomad_exomes_homozygous,
+                    exomes_hemizygous: query_gnomad_exomes_hemizygous,
+                    ..Default::default()
+                },
                 ..Default::default()
             },
             ..Default::default()
@@ -246,15 +253,18 @@ mod test {
         #[case] query_gnomad_genomes_hemizygous: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::GnomadOptions;
+        use crate::seqvars::query::schema::{GnomadOptions, PopulationFrequencyOptions};
 
         let query = CaseQuery {
-            gnomad: GnomadOptions {
-                genomes_enabled: query_gnomad_genomes_enabled,
-                genomes_frequency: query_gnomad_genomes_frequency,
-                genomes_heterozygous: query_gnomad_genomes_heterozygous,
-                genomes_homozygous: query_gnomad_genomes_homozygous,
-                genomes_hemizygous: query_gnomad_genomes_hemizygous,
+            population_freqeuecy: PopulationFrequencyOptions {
+                gnomad: GnomadOptions {
+                    genomes_enabled: query_gnomad_genomes_enabled,
+                    genomes_frequency: query_gnomad_genomes_frequency,
+                    genomes_heterozygous: query_gnomad_genomes_heterozygous,
+                    genomes_homozygous: query_gnomad_genomes_homozygous,
+                    genomes_hemizygous: query_gnomad_genomes_hemizygous,
+                    ..Default::default()
+                },
                 ..Default::default()
             },
             ..Default::default()
@@ -343,14 +353,17 @@ mod test {
         #[case] query_helix_homoplasmic: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::HelixMtDbOptions;
+        use crate::seqvars::query::schema::{HelixMtDbOptions, PopulationFrequencyOptions};
 
         let query = CaseQuery {
-            helixmtdb: HelixMtDbOptions {
-                enabled: query_helix_enabled,
-                frequency: query_helix_frequency,
-                heteroplasmic: query_helix_heteroplasmic,
-                homoplasmic: query_helix_homoplasmic,
+            population_freqeuecy: PopulationFrequencyOptions {
+                helixmtdb: HelixMtDbOptions {
+                    enabled: query_helix_enabled,
+                    frequency: query_helix_frequency,
+                    heteroplasmic: query_helix_heteroplasmic,
+                    homoplasmic: query_helix_homoplasmic,
+                },
+                ..Default::default()
             },
             ..Default::default()
         };
@@ -438,14 +451,17 @@ mod test {
         #[case] query_gnomad_genomes_homoplasmic: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::GnomadOptions;
+        use crate::seqvars::query::schema::{GnomadOptions, PopulationFrequencyOptions};
 
         let query = CaseQuery {
-            gnomad: GnomadOptions {
-                genomes_enabled: query_gnomad_genomes_enabled,
-                genomes_frequency: query_gnomad_genomes_frequency,
-                genomes_heterozygous: query_gnomad_genomes_heteroplasmic,
-                genomes_homozygous: query_gnomad_genomes_homoplasmic,
+            population_freqeuecy: PopulationFrequencyOptions {
+                gnomad: GnomadOptions {
+                    genomes_enabled: query_gnomad_genomes_enabled,
+                    genomes_frequency: query_gnomad_genomes_frequency,
+                    genomes_heterozygous: query_gnomad_genomes_heteroplasmic,
+                    genomes_homozygous: query_gnomad_genomes_homoplasmic,
+                    ..Default::default()
+                },
                 ..Default::default()
             },
             ..Default::default()
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index d7034f74..298cbac4 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -168,6 +168,23 @@ pub struct ClinVarOptions {
     pub include_conflicting_classifications: bool,
 }
 
+serde_with::with_prefix!(prefix_inhouse "inhouse_");
+#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
+#[serde(default)]
+/// TODO: currently unused?
+pub struct InhouseFrequencyOptions {
+    /// Whether to enable filtration by 1000 Genomes.
+    pub enabled: bool,
+    /// Maximal number of in-house carriers.
+    pub carriers: Option<i32>,
+    /// Maximal number of in-house heterozygous carriers.
+    pub heterozygous: Option<i32>,
+    /// Maximal number of in-house homozygous carriers.
+    pub homozygous: Option<i32>,
+    /// Maximal number of in-house hemizygous carriers.
+    pub hemizygous: Option<i32>,
+}
+
 serde_with::with_prefix!(prefix_gnomad "gnomad_");
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -196,23 +213,6 @@ pub struct GnomadOptions {
     pub genomes_hemizygous: Option<i32>,
 }
 
-serde_with::with_prefix!(prefix_inhouse "inhouse_");
-#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
-#[serde(default)]
-/// TODO: currently unused?
-pub struct InhouseOptions {
-    /// Whether to enable filtration by 1000 Genomes.
-    pub enabled: bool,
-    /// Maximal number of in-house carriers.
-    pub carriers: Option<i32>,
-    /// Maximal number of in-house heterozygous carriers.
-    pub heterozygous: Option<i32>,
-    /// Maximal number of in-house homozygous carriers.
-    pub homozygous: Option<i32>,
-    /// Maximal number of in-house hemizygous carriers.
-    pub hemizygous: Option<i32>,
-}
-
 serde_with::with_prefix!(prefix_helixmtdb "helixmtdb_");
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -228,7 +228,14 @@ pub struct HelixMtDbOptions {
     pub homoplasmic: Option<i32>,
 }
 
-
+#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
+#[serde(default)]
+pub struct PopulationFrequencyOptions {
+    #[serde(flatten, with = "prefix_gnomad")]
+    pub gnomad: GnomadOptions,
+    #[serde(flatten, with = "prefix_helixmtdb")]
+    pub helixmtdb: HelixMtDbOptions,
+}
 
 /// Data structure with a single query.
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
@@ -242,10 +249,15 @@ pub struct CaseQuery {
     /// Genotype choice for each individual.
     pub genotype: indexmap::IndexMap<String, Option<GenotypeChoice>>,
 
+    /// TODO v move to transcriptRealated
     /// Whether to include coding transcripts.
     pub transcripts_coding: bool,
     /// Whether to include non-coding transcripts.
     pub transcripts_noncoding: bool,
+    /// Maximal distance to next exon, if any.
+    pub max_exon_dist: Option<i32>,
+
+    /// TODO v move to varianttyperelated
 
     /// Whether to include SNVs.
     pub var_type_snv: bool,
@@ -254,8 +266,7 @@ pub struct CaseQuery {
     /// Whether to include MNVs.
     pub var_type_mnv: bool,
 
-    /// Maximal distance to next exon, if any.
-    pub max_exon_dist: Option<i32>,
+    /// TODO v Move to locusRelated
 
     /// List of HGNC symbols, HGNC:<ID>s, ENSG<ID>s, or NCBI Gene IDs to restrict
     /// the resulting variants to.
@@ -270,14 +281,15 @@ pub struct CaseQuery {
     /// ClinVar related filter options.
     #[serde(flatten, with = "prefix_clinvar")]
     pub clinvar: ClinVarOptions,
-    /// GnomAD related filter options.
-    #[serde(flatten, with = "prefix_gnomad")]
-    pub gnomad: GnomadOptions,
+
+    /// PopulationFrequency related filter options
+    #[serde(flatten)]
+    pub population_freqeuecy: PopulationFrequencyOptions,
+
+
     /// Inhouse related filter options. TODO BETTER COMMENT
     #[serde(flatten, with = "prefix_inhouse")]
-    pub inhouse: InhouseOptions,
-    #[serde(flatten, with = "prefix_helixmtdb")]
-    pub helixmtdb: HelixMtDbOptions,
+    pub inhouse: InhouseFrequencyOptions,
 }
 
 impl Default for ClinVarOptions {
@@ -298,7 +310,7 @@ impl Default for CaseQuery {
     fn default() -> Self {
         Self {
             consequences: mehari::annotate::seqvars::ann::Consequence::all(),
-            helixmtdb: Default::default(),
+            population_freqeuecy: Default::default(),
             quality: Default::default(),
             genotype: Default::default(),
             transcripts_coding: true,
@@ -311,7 +323,6 @@ impl Default for CaseQuery {
             genomic_regions: Default::default(),
             require_in_clinvar: Default::default(),
             clinvar: Default::default(),
-            gnomad: Default::default(),
             inhouse: Default::default(),
         }
     }
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
index 4e61283a..8bf87bff 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
@@ -56,10 +56,10 @@ quality: {}
 genotype: {}
 transcripts_coding: true
 transcripts_noncoding: true
+max_exon_dist: ~
 var_type_snv: true
 var_type_indel: true
 var_type_mnv: true
-max_exon_dist: ~
 gene_allowlist: ~
 genomic_regions: ~
 require_in_clinvar: false
@@ -79,12 +79,12 @@ gnomad_genomes_frequency: ~
 gnomad_genomes_heterozygous: ~
 gnomad_genomes_homozygous: ~
 gnomad_genomes_hemizygous: ~
+helixmtdb_enabled: false
+helixmtdb_frequency: ~
+helixmtdb_heteroplasmic: ~
+helixmtdb_homoplasmic: ~
 inhouse_enabled: false
 inhouse_carriers: ~
 inhouse_heterozygous: ~
 inhouse_homozygous: ~
 inhouse_hemizygous: ~
-helixmtdb_enabled: false
-helixmtdb_frequency: ~
-helixmtdb_heteroplasmic: ~
-helixmtdb_homoplasmic: ~
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
index 4c92ff1f..218169ac 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
@@ -65,10 +65,10 @@ genotype:
   sample: het
 transcripts_coding: true
 transcripts_noncoding: true
+max_exon_dist: 100
 var_type_snv: true
 var_type_indel: true
 var_type_mnv: true
-max_exon_dist: 100
 gene_allowlist: []
 genomic_regions: ~
 require_in_clinvar: false
@@ -88,12 +88,12 @@ gnomad_genomes_frequency: 0.002
 gnomad_genomes_heterozygous: 4
 gnomad_genomes_homozygous: 0
 gnomad_genomes_hemizygous: ~
+helixmtdb_enabled: true
+helixmtdb_frequency: 0.01
+helixmtdb_heteroplasmic: ~
+helixmtdb_homoplasmic: ~
 inhouse_enabled: true
 inhouse_carriers: 20
 inhouse_heterozygous: ~
 inhouse_homozygous: ~
 inhouse_hemizygous: ~
-helixmtdb_enabled: true
-helixmtdb_frequency: 0.01
-helixmtdb_heteroplasmic: ~
-helixmtdb_homoplasmic: ~
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
index 4c92ff1f..218169ac 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
@@ -65,10 +65,10 @@ genotype:
   sample: het
 transcripts_coding: true
 transcripts_noncoding: true
+max_exon_dist: 100
 var_type_snv: true
 var_type_indel: true
 var_type_mnv: true
-max_exon_dist: 100
 gene_allowlist: []
 genomic_regions: ~
 require_in_clinvar: false
@@ -88,12 +88,12 @@ gnomad_genomes_frequency: 0.002
 gnomad_genomes_heterozygous: 4
 gnomad_genomes_homozygous: 0
 gnomad_genomes_hemizygous: ~
+helixmtdb_enabled: true
+helixmtdb_frequency: 0.01
+helixmtdb_heteroplasmic: ~
+helixmtdb_homoplasmic: ~
 inhouse_enabled: true
 inhouse_carriers: 20
 inhouse_heterozygous: ~
 inhouse_homozygous: ~
 inhouse_hemizygous: ~
-helixmtdb_enabled: true
-helixmtdb_frequency: 0.01
-helixmtdb_heteroplasmic: ~
-helixmtdb_homoplasmic: ~

From 9b6b6baf37088a8a6b05ac09361874ce29f3f0f0 Mon Sep 17 00:00:00 2001
From: = <=>
Date: Sat, 29 Jun 2024 06:10:00 +0200
Subject: [PATCH 04/23] chore: more restructuring

---
 .../query/interpreter/regions_allowlist.rs    |  2 +-
 src/seqvars/query/mod.rs                      |  2 +-
 src/seqvars/query/schema.rs                   | 64 ++++++++++++-------
 3 files changed, 43 insertions(+), 25 deletions(-)

diff --git a/src/seqvars/query/interpreter/regions_allowlist.rs b/src/seqvars/query/interpreter/regions_allowlist.rs
index 0fcd4965..9fff9378 100644
--- a/src/seqvars/query/interpreter/regions_allowlist.rs
+++ b/src/seqvars/query/interpreter/regions_allowlist.rs
@@ -2,7 +2,7 @@ use crate::seqvars::query::schema::{CaseQuery, GenomicRegion, Range, SequenceVar
 
 /// Determine whether the `SequenceVariant` passes the regions allowlist filter.
 pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> bool {
-    if let Some(region_allowlist) = &query.genomic_regions {
+    if let Some(region_allowlist) = &query.locus.genomic_regions {
         if region_allowlist.is_empty() {
             true
         } else {
diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs
index b4b6e2bf..774286d0 100644
--- a/src/seqvars/query/mod.rs
+++ b/src/seqvars/query/mod.rs
@@ -520,7 +520,7 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
     trace_rss_now();
 
     tracing::info!("Translating gene allow list...");
-    let hgnc_allowlist = if let Some(gene_allowlist) = &query.gene_allowlist {
+    let hgnc_allowlist = if let Some(gene_allowlist) = &query.locus.gene_allowlist {
         if gene_allowlist.is_empty() {
             None
         } else {
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 298cbac4..32a9dedd 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -237,6 +237,38 @@ pub struct PopulationFrequencyOptions {
     pub helixmtdb: HelixMtDbOptions,
 }
 
+serde_with::with_prefix!(prefix_var_type "var_type_");
+#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
+#[serde(default)]
+pub struct VariantTypeOptions {
+    /// Whether to include SNVs.
+    pub snv: bool,
+    /// Whether to include indels.
+    pub indel: bool,
+    /// Whether to include MNVs.
+    pub mnv: bool,
+}
+
+impl Default for VariantTypeOptions {
+    fn default() -> Self {
+        VariantTypeOptions {
+            snv: true,
+            indel: true,
+            mnv: true,
+        }
+    }
+}
+
+#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
+#[serde(default)]
+pub struct LocusRelatedOptions {
+    /// List of HGNC symbols, HGNC:<ID>s, ENSG<ID>s, or NCBI Gene IDs to restrict
+    /// the resulting variants to.
+    pub gene_allowlist: Option<Vec<String>>,
+    /// List of genomic regions to limit restrict the resulting variants to.
+    pub genomic_regions: Option<Vec<GenomicRegion>>,
+}
+
 /// Data structure with a single query.
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -257,25 +289,15 @@ pub struct CaseQuery {
     /// Maximal distance to next exon, if any.
     pub max_exon_dist: Option<i32>,
 
-    /// TODO v move to varianttyperelated
-
-    /// Whether to include SNVs.
-    pub var_type_snv: bool,
-    /// Whether to include indels.
-    pub var_type_indel: bool,
-    /// Whether to include MNVs.
-    pub var_type_mnv: bool,
-
-    /// TODO v Move to locusRelated
+    /// TODO: comment
+    #[serde(flatten, with = "prefix_var_type")]
+    pub var_type: VariantTypeOptions,
 
-    /// List of HGNC symbols, HGNC:<ID>s, ENSG<ID>s, or NCBI Gene IDs to restrict
-    /// the resulting variants to.
-    pub gene_allowlist: Option<Vec<String>>,
-    /// List of genomic regions to limit restrict the resulting variants to.
-    pub genomic_regions: Option<Vec<GenomicRegion>>,
-
-    /// TODO: wanted schema is defined in issue, emily reading comprehension 10/10
+    /// TODO comment
+    #[serde(flatten)]
+    pub locus: LocusRelatedOptions,
 
+    // TODO v moving this into ClinVarOptions without making things meh seems to be annoying
     /// Wether to require ClinVar membership.
     pub require_in_clinvar: bool,
     /// ClinVar related filter options.
@@ -286,7 +308,6 @@ pub struct CaseQuery {
     #[serde(flatten)]
     pub population_freqeuecy: PopulationFrequencyOptions,
 
-
     /// Inhouse related filter options. TODO BETTER COMMENT
     #[serde(flatten, with = "prefix_inhouse")]
     pub inhouse: InhouseFrequencyOptions,
@@ -315,12 +336,9 @@ impl Default for CaseQuery {
             genotype: Default::default(),
             transcripts_coding: true,
             transcripts_noncoding: true,
-            var_type_snv: true,
-            var_type_indel: true,
-            var_type_mnv: true,
+            var_type: Default::default(),
             max_exon_dist: Default::default(),
-            gene_allowlist: Default::default(),
-            genomic_regions: Default::default(),
+            locus: Default::default(),
             require_in_clinvar: Default::default(),
             clinvar: Default::default(),
             inhouse: Default::default(),

From 2f26227f53971c47b14399a3d21209e1268ba4c3 Mon Sep 17 00:00:00 2001
From: = <=>
Date: Mon, 1 Jul 2024 05:16:05 +0200
Subject: [PATCH 05/23] chore: casequery now has schema as defined in #374

---
 src/seqvars/query/schema.rs | 35 +++++++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 10 deletions(-)

diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 32a9dedd..160ac7a8 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -269,6 +269,27 @@ pub struct LocusRelatedOptions {
     pub genomic_regions: Option<Vec<GenomicRegion>>,
 }
 
+#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
+#[serde(default)]
+pub struct TranscriptOptions {
+    /// Whether to include coding transcripts.
+    pub transcripts_coding: bool,
+    /// Whether to include non-coding transcripts.
+    pub transcripts_noncoding: bool,
+    /// Maximal distance to next exon, if any.
+    pub max_exon_dist: Option<i32>,
+}
+
+impl Default for TranscriptOptions {
+    fn default() -> Self {
+        TranscriptOptions {
+            transcripts_coding: true,
+            transcripts_noncoding: true,
+            max_exon_dist: Default::default(),
+        }
+    }
+}
+
 /// Data structure with a single query.
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -281,13 +302,9 @@ pub struct CaseQuery {
     /// Genotype choice for each individual.
     pub genotype: indexmap::IndexMap<String, Option<GenotypeChoice>>,
 
-    /// TODO v move to transcriptRealated
-    /// Whether to include coding transcripts.
-    pub transcripts_coding: bool,
-    /// Whether to include non-coding transcripts.
-    pub transcripts_noncoding: bool,
-    /// Maximal distance to next exon, if any.
-    pub max_exon_dist: Option<i32>,
+    /// TODO: comment
+    #[serde(flatten)]
+    pub transcript: TranscriptOptions,
 
     /// TODO: comment
     #[serde(flatten, with = "prefix_var_type")]
@@ -334,10 +351,8 @@ impl Default for CaseQuery {
             population_freqeuecy: Default::default(),
             quality: Default::default(),
             genotype: Default::default(),
-            transcripts_coding: true,
-            transcripts_noncoding: true,
+            transcript: Default::default(),
             var_type: Default::default(),
-            max_exon_dist: Default::default(),
             locus: Default::default(),
             require_in_clinvar: Default::default(),
             clinvar: Default::default(),

From c78d78e7a3b1078443fd1008fc270d1b139249b5 Mon Sep 17 00:00:00 2001
From: = <=>
Date: Wed, 3 Jul 2024 05:48:00 +0200
Subject: [PATCH 06/23] chore: fix typo

---
 src/seqvars/query/interpreter/frequency.rs | 10 +++++-----
 src/seqvars/query/schema.rs                |  6 ++++--
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs
index 292917ef..974429ac 100644
--- a/src/seqvars/query/interpreter/frequency.rs
+++ b/src/seqvars/query/interpreter/frequency.rs
@@ -2,7 +2,7 @@ use crate::seqvars::query::schema::{CaseQuery, SequenceVariant};
 
 /// Determine whether the `SequenceVariant` passes the frequency filter.
 pub fn passes(query: &CaseQuery, s: &SequenceVariant) -> Result<bool, anyhow::Error> {
-    let pop = &query.population_freqeuecy;
+    let pop = &query.population_frequency;
     let is_mtdna = annonars::common::cli::canonicalize(&s.chrom) == "MT";
 
     if is_mtdna {
@@ -137,7 +137,7 @@ mod test {
         use crate::seqvars::query::schema::{GnomadOptions, PopulationFrequencyOptions};
 
         let query = CaseQuery {
-            population_freqeuecy: PopulationFrequencyOptions {
+            population_frequency: PopulationFrequencyOptions {
                 gnomad: GnomadOptions {
                     exomes_enabled: query_gnomad_exomes_enabled,
                     exomes_frequency: query_gnomad_exomes_frequency,
@@ -256,7 +256,7 @@ mod test {
         use crate::seqvars::query::schema::{GnomadOptions, PopulationFrequencyOptions};
 
         let query = CaseQuery {
-            population_freqeuecy: PopulationFrequencyOptions {
+            population_frequency: PopulationFrequencyOptions {
                 gnomad: GnomadOptions {
                     genomes_enabled: query_gnomad_genomes_enabled,
                     genomes_frequency: query_gnomad_genomes_frequency,
@@ -356,7 +356,7 @@ mod test {
         use crate::seqvars::query::schema::{HelixMtDbOptions, PopulationFrequencyOptions};
 
         let query = CaseQuery {
-            population_freqeuecy: PopulationFrequencyOptions {
+            population_frequency: PopulationFrequencyOptions {
                 helixmtdb: HelixMtDbOptions {
                     enabled: query_helix_enabled,
                     frequency: query_helix_frequency,
@@ -454,7 +454,7 @@ mod test {
         use crate::seqvars::query::schema::{GnomadOptions, PopulationFrequencyOptions};
 
         let query = CaseQuery {
-            population_freqeuecy: PopulationFrequencyOptions {
+            population_frequency: PopulationFrequencyOptions {
                 gnomad: GnomadOptions {
                     genomes_enabled: query_gnomad_genomes_enabled,
                     genomes_frequency: query_gnomad_genomes_frequency,
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 160ac7a8..8894c58a 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -323,7 +323,7 @@ pub struct CaseQuery {
 
     /// PopulationFrequency related filter options
     #[serde(flatten)]
-    pub population_freqeuecy: PopulationFrequencyOptions,
+    pub population_frequency: PopulationFrequencyOptions,
 
     /// Inhouse related filter options. TODO BETTER COMMENT
     #[serde(flatten, with = "prefix_inhouse")]
@@ -348,7 +348,7 @@ impl Default for CaseQuery {
     fn default() -> Self {
         Self {
             consequences: mehari::annotate::seqvars::ann::Consequence::all(),
-            population_freqeuecy: Default::default(),
+            population_frequency: Default::default(),
             quality: Default::default(),
             genotype: Default::default(),
             transcript: Default::default(),
@@ -652,6 +652,8 @@ impl SequenceVariant {
         if self.gnomad_genomes_an == 0 {
             return 0f32;
         }
+        // TODO, emily: is this code hot then check v   
+        // This code looks like it could result in some missed oppportunity for optimisation, is it really necessary for hom het and hemi to ever be floats?
         let an = self.gnomad_genomes_an as f32;
         let hom = self.gnomad_genomes_hom as f32;
         let het = self.gnomad_genomes_het as f32;

From 815f233ed58ffe13069fbc81e173801dd1d9a9dd Mon Sep 17 00:00:00 2001
From: = <=>
Date: Wed, 3 Jul 2024 06:28:17 +0200
Subject: [PATCH 07/23] chore: work on sequencevariant layout

---
 src/seqvars/query/interpreter/frequency.rs  |  91 ++++++++++----
 src/seqvars/query/output/variant_related.rs |  28 ++---
 src/seqvars/query/schema.rs                 | 130 ++++++++++++--------
 3 files changed, 159 insertions(+), 90 deletions(-)

diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs
index 974429ac..52fb9849 100644
--- a/src/seqvars/query/interpreter/frequency.rs
+++ b/src/seqvars/query/interpreter/frequency.rs
@@ -10,9 +10,11 @@ pub fn passes(query: &CaseQuery, s: &SequenceVariant) -> Result<bool, anyhow::Er
             && (pop.helixmtdb.frequency.is_some()
                 && s.helixmtdb_af() > pop.helixmtdb.frequency.expect("tested before")
                 || pop.helixmtdb.heteroplasmic.is_some()
-                    && s.helix_het > pop.helixmtdb.heteroplasmic.expect("tested before")
+                    && s.population_frequencies.helixmtdb.het
+                        > pop.helixmtdb.heteroplasmic.expect("tested before")
                 || pop.helixmtdb.homoplasmic.is_some()
-                    && s.helix_hom > pop.helixmtdb.homoplasmic.expect("tested before"))
+                    && s.population_frequencies.helixmtdb.hom
+                        > pop.helixmtdb.homoplasmic.expect("tested before"))
         {
             tracing::trace!(
                 "variant {:?} fails HelixMtDb frequency filter {:?}",
@@ -25,11 +27,14 @@ pub fn passes(query: &CaseQuery, s: &SequenceVariant) -> Result<bool, anyhow::Er
         && (pop.gnomad.exomes_frequency.is_some()
             && s.gnomad_exomes_af() > pop.gnomad.exomes_frequency.expect("tested before")
             || pop.gnomad.exomes_heterozygous.is_some()
-                && s.gnomad_exomes_het > pop.gnomad.exomes_heterozygous.expect("tested before")
+                && s.population_frequencies.gnomad.exomes_het
+                    > pop.gnomad.exomes_heterozygous.expect("tested before")
             || pop.gnomad.exomes_homozygous.is_some()
-                && s.gnomad_exomes_hom > pop.gnomad.exomes_homozygous.expect("tested before")
+                && s.population_frequencies.gnomad.exomes_hom
+                    > pop.gnomad.exomes_homozygous.expect("tested before")
             || pop.gnomad.exomes_hemizygous.is_some()
-                && s.gnomad_exomes_hemi > pop.gnomad.exomes_hemizygous.expect("tested before"))
+                && s.population_frequencies.gnomad.exomes_hemi
+                    > pop.gnomad.exomes_hemizygous.expect("tested before"))
     {
         tracing::trace!(
             "variant {:?} fails gnomAD exomes frequency filter {:?}",
@@ -43,12 +48,15 @@ pub fn passes(query: &CaseQuery, s: &SequenceVariant) -> Result<bool, anyhow::Er
         && (pop.gnomad.genomes_frequency.is_some()
             && s.gnomad_genomes_af() > pop.gnomad.genomes_frequency.expect("tested before")
             || pop.gnomad.genomes_heterozygous.is_some()
-                && s.gnomad_genomes_het > pop.gnomad.genomes_heterozygous.expect("tested before")
+                && s.population_frequencies.gnomad.genomes_het
+                    > pop.gnomad.genomes_heterozygous.expect("tested before")
             || pop.gnomad.genomes_homozygous.is_some()
-                && s.gnomad_genomes_hom > pop.gnomad.genomes_homozygous.expect("tested before")
+                && s.population_frequencies.gnomad.genomes_hom
+                    > pop.gnomad.genomes_homozygous.expect("tested before")
             || !is_mtdna
                 && pop.gnomad.genomes_hemizygous.is_some()
-                && s.gnomad_genomes_hemi > pop.gnomad.genomes_hemizygous.expect("tested before"))
+                && s.population_frequencies.gnomad.genomes_hemi
+                    > pop.gnomad.genomes_hemizygous.expect("tested before"))
     {
         tracing::trace!(
             "variant {:?} fails gnomAD genomes frequency filter {:?}",
@@ -67,7 +75,9 @@ mod test {
     use mehari::annotate::seqvars::ann::{AnnField, Consequence};
     use rstest::rstest;
 
-    use crate::seqvars::query::schema::{CaseQuery, SequenceVariant};
+    use crate::seqvars::query::schema::{
+        CaseQuery, HelixMtDBs, PopulationFrequencies, SequenceVariant,
+    };
 
     #[rstest]
     // -- frequency ---------------------------------------------------------
@@ -134,7 +144,9 @@ mod test {
         #[case] query_gnomad_exomes_hemizygous: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::{GnomadOptions, PopulationFrequencyOptions};
+        use crate::seqvars::query::schema::{
+            GnomadOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
+        };
 
         let query = CaseQuery {
             population_frequency: PopulationFrequencyOptions {
@@ -151,10 +163,16 @@ mod test {
             ..Default::default()
         };
         let seq_var = SequenceVariant {
-            gnomad_exomes_an: seqvar_gnomad_exomes_an,
-            gnomad_exomes_het: seqvar_gnomad_exomes_het,
-            gnomad_exomes_hom: seqvar_gnomad_exomes_hom,
-            gnomad_exomes_hemi: seqvar_gnomad_exomes_hemi,
+            population_frequencies: PopulationFrequencies {
+                gnomad: Gnomads {
+                    exomes_an: seqvar_gnomad_exomes_an,
+                    exomes_het: seqvar_gnomad_exomes_het,
+                    exomes_hom: seqvar_gnomad_exomes_hom,
+                    exomes_hemi: seqvar_gnomad_exomes_hemi,
+                    ..Default::default()
+                },
+                ..Default::default()
+            },
             chrom: "X".to_string(),
             reference: "G".into(),
             alternative: "A".into(),
@@ -253,7 +271,9 @@ mod test {
         #[case] query_gnomad_genomes_hemizygous: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::{GnomadOptions, PopulationFrequencyOptions};
+        use crate::seqvars::query::schema::{
+            GnomadOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
+        };
 
         let query = CaseQuery {
             population_frequency: PopulationFrequencyOptions {
@@ -270,10 +290,16 @@ mod test {
             ..Default::default()
         };
         let seq_var = SequenceVariant {
-            gnomad_genomes_an: seqvar_gnomad_genomes_an,
-            gnomad_genomes_het: seqvar_gnomad_genomes_het,
-            gnomad_genomes_hom: seqvar_gnomad_genomes_hom,
-            gnomad_genomes_hemi: seqvar_gnomad_genomes_hemi,
+            population_frequencies: PopulationFrequencies {
+                gnomad: Gnomads {
+                    genomes_an: seqvar_gnomad_genomes_an,
+                    genomes_het: seqvar_gnomad_genomes_het,
+                    genomes_hom: seqvar_gnomad_genomes_hom,
+                    genomes_hemi: seqvar_gnomad_genomes_hemi,
+                    ..Default::default()
+                },
+                ..Default::default()
+            },
             chrom: "X".to_string(),
             reference: "G".into(),
             alternative: "A".into(),
@@ -368,9 +394,14 @@ mod test {
             ..Default::default()
         };
         let seq_var = SequenceVariant {
-            helix_an: seqvar_helix_an,
-            helix_het: seqvar_helix_het,
-            helix_hom: seqvar_helix_hom,
+            population_frequencies: PopulationFrequencies {
+                helixmtdb: HelixMtDBs {
+                    an: seqvar_helix_an,
+                    het: seqvar_helix_het,
+                    hom: seqvar_helix_hom,
+                },
+                ..Default::default()
+            },
             chrom: "MT".to_string(),
             reference: "G".into(),
             alternative: "A".into(),
@@ -451,7 +482,9 @@ mod test {
         #[case] query_gnomad_genomes_homoplasmic: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::{GnomadOptions, PopulationFrequencyOptions};
+        use crate::seqvars::query::schema::{
+            GnomadOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
+        };
 
         let query = CaseQuery {
             population_frequency: PopulationFrequencyOptions {
@@ -467,9 +500,15 @@ mod test {
             ..Default::default()
         };
         let seq_var = SequenceVariant {
-            gnomad_genomes_an: seqvar_gnomad_genomes_an,
-            gnomad_genomes_het: seqvar_gnomad_genomes_het,
-            gnomad_genomes_hom: seqvar_gnomad_genomes_hom,
+            population_frequencies: PopulationFrequencies {
+                gnomad: Gnomads {
+                    genomes_an: seqvar_gnomad_genomes_an,
+                    genomes_het: seqvar_gnomad_genomes_het,
+                    genomes_hom: seqvar_gnomad_genomes_hom,
+                    ..Default::default()
+                },
+                ..Default::default()
+            },
             chrom: "MT".to_string(),
             reference: "G".into(),
             alternative: "A".into(),
diff --git a/src/seqvars/query/output/variant_related.rs b/src/seqvars/query/output/variant_related.rs
index 8e18ba61..6359f663 100644
--- a/src/seqvars/query/output/variant_related.rs
+++ b/src/seqvars/query/output/variant_related.rs
@@ -398,20 +398,20 @@ impl Frequency {
                 .gnomad_genomes(
                     NuclearFrequency::new(
                         seqvar.gnomad_genomes_af(),
-                        seqvar.gnomad_genomes_an,
-                        seqvar.gnomad_genomes_het,
-                        seqvar.gnomad_genomes_hom,
-                        seqvar.gnomad_genomes_hemi,
+                        seqvar.population_frequencies.gnomad.genomes_an,
+                        seqvar.population_frequencies.gnomad.genomes_het,
+                        seqvar.population_frequencies.gnomad.genomes_hom,
+                        seqvar.population_frequencies.gnomad.genomes_hemi,
                     )
                     .some_unless_empty(),
                 )
                 .gnomad_exomes(
                     NuclearFrequency::new(
                         seqvar.gnomad_exomes_af(),
-                        seqvar.gnomad_exomes_an,
-                        seqvar.gnomad_exomes_het,
-                        seqvar.gnomad_exomes_hom,
-                        seqvar.gnomad_exomes_hemi,
+                        seqvar.population_frequencies.gnomad.exomes_an,
+                        seqvar.population_frequencies.gnomad.exomes_het,
+                        seqvar.population_frequencies.gnomad.exomes_hom,
+                        seqvar.population_frequencies.gnomad.exomes_hemi,
                     )
                     .some_unless_empty(),
                 )
@@ -421,18 +421,18 @@ impl Frequency {
                 .gnomad_mtdna(
                     MtdnaFrequency::new(
                         seqvar.gnomad_genomes_af(),
-                        seqvar.gnomad_genomes_an,
-                        seqvar.gnomad_genomes_het,
-                        seqvar.gnomad_genomes_hom,
+                        seqvar.population_frequencies.gnomad.genomes_an,
+                        seqvar.population_frequencies.gnomad.genomes_het,
+                        seqvar.population_frequencies.gnomad.genomes_hom,
                     )
                     .some_unless_empty(),
                 )
                 .helixmtdb(
                     MtdnaFrequency::new(
                         seqvar.helixmtdb_af(),
-                        seqvar.helix_an,
-                        seqvar.helix_het,
-                        seqvar.helix_hom,
+                        seqvar.population_frequencies.helixmtdb.an,
+                        seqvar.population_frequencies.helixmtdb.het,
+                        seqvar.population_frequencies.helixmtdb.hom,
                     )
                     .some_unless_empty(),
                 )
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 8894c58a..459e3f4f 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -407,6 +407,50 @@ pub struct CallInfo {
     pub phasing_id: Option<i32>,
 }
 
+// serde_with::with_prefix!(prefix_gnomad "gnomad_"); < already declared earlier
+#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
+pub struct Gnomads {
+    /// Number of alleles in gnomAD exomes (not for chrMT).
+    pub exomes_an: i32,
+    /// Number of homozygous carriers in gnomAD exomes (not for chrMT).
+    pub exomes_hom: i32,
+    /// Number of heterozygous carriers in gnomAD exomes (not for chrMT).
+    pub exomes_het: i32,
+    /// Number of hemizygous carriers in gnomAD exomes (not for chrMT).
+    pub exomes_hemi: i32,
+
+    /// Number of alleles in gnomAD genomes (also for chrMT).
+    pub genomes_an: i32,
+    /// Number of homozygous carriers in gnomAD genomes (also for chrMT).
+    pub genomes_hom: i32,
+    /// Number of heterozygous carriers in gnomAD genomes (also for chrMT).
+    pub genomes_het: i32,
+    /// Number of hemizygous carriers in gnomAD genomes (not for chrMT).
+    pub genomes_hemi: i32,
+}
+
+// Name difference due to legacy json
+serde_with::with_prefix!(prefix_helix "helix_");
+
+#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
+pub struct HelixMtDBs {
+    /// Number of alleles in HelixMtDb cohort (only chrMT).
+    pub an: i32,
+    /// Number of homoplasmic carriers in HelixMtDb cohort (only chrMT).
+    pub hom: i32,
+    /// Number of heteroplasmic carriers in HelixMtDb cohort (only chrMT).
+    pub het: i32,
+}
+
+#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
+
+pub struct PopulationFrequencies {
+    #[serde(flatten, with = "prefix_gnomad")]
+    pub gnomad: Gnomads,
+    #[serde(flatten, with = "prefix_helix")]
+    pub helixmtdb: HelixMtDBs,
+}
+
 /// Definition of a sequence variant with per-sample genotype calls.
 ///
 /// This uses a subset/specialization of what is described by the VCF standard
@@ -426,30 +470,9 @@ pub struct SequenceVariant {
     /// Variant effect annotation.
     pub ann_fields: Vec<mehari::annotate::seqvars::ann::AnnField>,
 
-    /// Number of alleles in gnomAD exomes (not for chrMT).
-    pub gnomad_exomes_an: i32,
-    /// Number of homozygous carriers in gnomAD exomes (not for chrMT).
-    pub gnomad_exomes_hom: i32,
-    /// Number of heterozygous carriers in gnomAD exomes (not for chrMT).
-    pub gnomad_exomes_het: i32,
-    /// Number of hemizygous carriers in gnomAD exomes (not for chrMT).
-    pub gnomad_exomes_hemi: i32,
-
-    /// Number of alleles in gnomAD genomes (also for chrMT).
-    pub gnomad_genomes_an: i32,
-    /// Number of homozygous carriers in gnomAD genomes (also for chrMT).
-    pub gnomad_genomes_hom: i32,
-    /// Number of heterozygous carriers in gnomAD genomes (also for chrMT).
-    pub gnomad_genomes_het: i32,
-    /// Number of hemizygous carriers in gnomAD genomes (not for chrMT).
-    pub gnomad_genomes_hemi: i32,
-
-    /// Number of alleles in HelixMtDb cohort (only chrMT).
-    pub helix_an: i32,
-    /// Number of homoplasmic carriers in HelixMtDb cohort (only chrMT).
-    pub helix_hom: i32,
-    /// Number of heteroplasmic carriers in HelixMtDb cohort (only chrMT).
-    pub helix_het: i32,
+    /// TODO: comment
+    #[serde(flatten)]
+    pub population_frequencies: PopulationFrequencies,
 
     /// Number of in-house alleles (also for chrMT).
     pub inhouse_an: i32,
@@ -620,55 +643,62 @@ impl SequenceVariant {
         extract_key!(helix_het);
 
         Ok(SequenceVariant {
-            gnomad_exomes_an,
-            gnomad_exomes_hom,
-            gnomad_exomes_het,
-            gnomad_exomes_hemi,
-            gnomad_genomes_an,
-            gnomad_genomes_hom,
-            gnomad_genomes_het,
-            gnomad_genomes_hemi,
-            helix_an,
-            helix_hom,
-            helix_het,
+            population_frequencies: PopulationFrequencies {
+                gnomad: Gnomads {
+                    exomes_an: gnomad_exomes_an,
+                    exomes_hom: gnomad_exomes_hom,
+                    exomes_het: gnomad_exomes_het,
+                    exomes_hemi: gnomad_exomes_hemi,
+
+                    genomes_an: gnomad_genomes_an,
+                    genomes_hom: gnomad_genomes_hom,
+                    genomes_het: gnomad_genomes_het,
+                    genomes_hemi: gnomad_genomes_hemi,
+                },
+                helixmtdb: HelixMtDBs {
+                    an: helix_an,
+                    hom: helix_hom,
+                    het: helix_het,
+                },
+            },
             ..result
         })
     }
 
     /// Return allele frequency in gnomAD exomes.
     pub fn gnomad_exomes_af(&self) -> f32 {
-        if self.gnomad_exomes_an == 0 {
+        if self.population_frequencies.gnomad.exomes_an == 0 {
             return 0f32;
         }
-        let an = self.gnomad_exomes_an as f32;
-        let hom = self.gnomad_exomes_hom as f32;
-        let het = self.gnomad_exomes_het as f32;
-        let hemi = self.gnomad_exomes_hemi as f32;
+        let an = self.population_frequencies.gnomad.exomes_an as f32;
+        let hom = self.population_frequencies.gnomad.exomes_hom as f32;
+        let het = self.population_frequencies.gnomad.exomes_het as f32;
+        let hemi = self.population_frequencies.gnomad.exomes_hemi as f32;
         (2.0 * hom + het + hemi) / an
     }
 
     /// Return allele frequency in gnomAD genomes.
     pub fn gnomad_genomes_af(&self) -> f32 {
-        if self.gnomad_genomes_an == 0 {
+        if self.population_frequencies.gnomad.genomes_an == 0 {
             return 0f32;
         }
-        // TODO, emily: is this code hot then check v   
+        // TODO, emily: is this code hot then check v
         // This code looks like it could result in some missed oppportunity for optimisation, is it really necessary for hom het and hemi to ever be floats?
-        let an = self.gnomad_genomes_an as f32;
-        let hom = self.gnomad_genomes_hom as f32;
-        let het = self.gnomad_genomes_het as f32;
-        let hemi = self.gnomad_genomes_hemi as f32;
+        let an = self.population_frequencies.gnomad.genomes_an as f32;
+        let hom = self.population_frequencies.gnomad.genomes_hom as f32;
+        let het = self.population_frequencies.gnomad.genomes_het as f32;
+        let hemi = self.population_frequencies.gnomad.genomes_hemi as f32;
         (2.0 * hom + het + hemi) / an
     }
 
     /// Return allele frequency in HelixMtDb.
     pub fn helixmtdb_af(&self) -> f32 {
-        if self.helix_an == 0 {
+        if self.population_frequencies.helixmtdb.an == 0 {
             return 0f32;
         }
-        let an = self.helix_an as f32;
-        let hom = self.helix_hom as f32;
-        let het = self.helix_het as f32;
+        let an = self.population_frequencies.helixmtdb.an as f32;
+        let hom = self.population_frequencies.helixmtdb.hom as f32;
+        let het = self.population_frequencies.helixmtdb.het as f32;
         (2.0 * hom + het) / an
     }
 }

From ddbd6acf07011e948ede356058e2bfd275f7221f Mon Sep 17 00:00:00 2001
From: = <=>
Date: Wed, 3 Jul 2024 06:47:00 +0200
Subject: [PATCH 08/23] chore: finish sequencevariant layout

---
 src/seqvars/query/schema.rs                   | 29 ++++++++++-------
 ...riant_from_vcf@Case_1.ingested.vcf-10.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-11.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-12.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-13.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-14.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-15.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-16.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-17.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-18.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-19.snap | 30 +++++++++---------
 ...ariant_from_vcf@Case_1.ingested.vcf-2.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-20.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-21.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-22.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-23.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-24.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-25.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-26.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-27.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-28.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-29.snap | 30 +++++++++---------
 ...ariant_from_vcf@Case_1.ingested.vcf-3.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-30.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-31.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-32.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-33.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-34.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-35.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-36.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-37.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-38.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-39.snap | 30 +++++++++---------
 ...ariant_from_vcf@Case_1.ingested.vcf-4.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-40.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-41.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-42.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-43.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-44.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-45.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-46.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-47.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-48.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-49.snap | 30 +++++++++---------
 ...ariant_from_vcf@Case_1.ingested.vcf-5.snap | 31 ++++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-50.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-51.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-52.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-53.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-54.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-55.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-56.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-57.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-58.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-59.snap | 30 +++++++++---------
 ...ariant_from_vcf@Case_1.ingested.vcf-6.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-60.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-61.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-62.snap | 30 +++++++++---------
 ...riant_from_vcf@Case_1.ingested.vcf-63.snap | 30 +++++++++---------
 ...ariant_from_vcf@Case_1.ingested.vcf-7.snap | 30 +++++++++---------
 ...ariant_from_vcf@Case_1.ingested.vcf-8.snap | 30 +++++++++---------
 ...ariant_from_vcf@Case_1.ingested.vcf-9.snap | 30 +++++++++---------
 ..._variant_from_vcf@Case_1.ingested.vcf.snap | 30 +++++++++---------
 ...ariant_from_vcf@dragen.ingested.vcf-2.snap | 14 ++++-----
 ..._variant_from_vcf@dragen.ingested.vcf.snap | 16 +++++-----
 66 files changed, 979 insertions(+), 971 deletions(-)

diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 459e3f4f..cfdf0a20 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -451,6 +451,19 @@ pub struct PopulationFrequencies {
     pub helixmtdb: HelixMtDBs,
 }
 
+// serde_with::with_prefix!(prefix_inhouse "inhouse_"); < already declared earlier
+#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
+pub struct InhouseFrequencies {
+    /// Number of in-house alleles (also for chrMT).
+    pub an: i32,
+    /// Number of homozygous carriers in in-house cohort (also for chrMT).
+    pub hom: i32,
+    /// Number of heterozygous carriers in in-house cohort (also for chrMT).
+    pub het: i32,
+    /// Number of hemizygous carriers in in-house cohort (not for chrMT).
+    pub hemi: i32,
+}
+
 /// Definition of a sequence variant with per-sample genotype calls.
 ///
 /// This uses a subset/specialization of what is described by the VCF standard
@@ -470,21 +483,15 @@ pub struct SequenceVariant {
     /// Variant effect annotation.
     pub ann_fields: Vec<mehari::annotate::seqvars::ann::AnnField>,
 
+    /// Mapping of sample to genotype information for the SV.
+    pub call_info: indexmap::IndexMap<String, CallInfo>,
+
     /// TODO: comment
     #[serde(flatten)]
     pub population_frequencies: PopulationFrequencies,
 
-    /// Number of in-house alleles (also for chrMT).
-    pub inhouse_an: i32,
-    /// Number of homozygous carriers in in-house cohort (also for chrMT).
-    pub inhouse_hom: i32,
-    /// Number of heterozygous carriers in in-house cohort (also for chrMT).
-    pub inhouse_het: i32,
-    /// Number of hemizygous carriers in in-house cohort (not for chrMT).
-    pub inhouse_hemi: i32,
-
-    /// Mapping of sample to genotype information for the SV.
-    pub call_info: indexmap::IndexMap<String, CallInfo>,
+    #[serde(flatten, with = "prefix_inhouse")]
+    pub inhouse_frequencies: InhouseFrequencies,
 }
 
 impl SequenceVariant {
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap
index 36665ee3..ead427e8 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap
@@ -120,21 +120,6 @@ ann_fields:
     protein_pos: ~
     distance: 2333
     messages: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -154,3 +139,18 @@ call_info:
     dp: 10
     ad: 5
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap
index d7e46d39..915b4386 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap
@@ -7,21 +7,6 @@ pos: 73
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 3320
     ad: 3320
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap
index a34b5fae..781b0139 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap
@@ -7,21 +7,6 @@ pos: 119
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 4113
     ad: 4112
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap
index 2c29e43a..ab498001 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap
@@ -7,21 +7,6 @@ pos: 189
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 2204
     ad: 2204
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap
index 2dac26d7..2d5a3119 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap
@@ -7,21 +7,6 @@ pos: 195
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1815
     ad: 1815
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap
index 03618eee..600682cb 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap
@@ -7,21 +7,6 @@ pos: 204
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1304
     ad: 1304
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap
index fc95bcb6..ff9c3f92 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap
@@ -7,21 +7,6 @@ pos: 207
 reference: G
 alternative: A
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1277
     ad: 1277
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap
index 17016a3e..4696d17d 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap
@@ -7,21 +7,6 @@ pos: 263
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 1031
     ad: 1031
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap
index d67debb3..3d05e063 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap
@@ -7,21 +7,6 @@ pos: 302
 reference: A
 alternative: ACC
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/1
@@ -41,3 +26,18 @@ call_info:
     dp: 803
     ad: 3
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap
index b31139fa..990786b9 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap
@@ -7,21 +7,6 @@ pos: 310
 reference: T
 alternative: TC
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 1091
     ad: 1090
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap
index 890407f6..9a87b987 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap
@@ -119,21 +119,6 @@ ann_fields:
     protein_pos: ~
     distance: -434
     messages: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -153,3 +138,18 @@ call_info:
     dp: 40
     ad: 21
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap
index 3cf8636e..6a7e3b22 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap
@@ -7,21 +7,6 @@ pos: 477
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 1725
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap
index 1838ec8f..dca82aa0 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap
@@ -7,21 +7,6 @@ pos: 709
 reference: G
 alternative: A
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1814
     ad: 1813
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap
index b51a4e7c..5aa61fec 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap
@@ -7,21 +7,6 @@ pos: 750
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 1621
     ad: 1621
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap
index 355a6d75..17d1f425 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap
@@ -7,21 +7,6 @@ pos: 879
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1898
     ad: 547
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap
index a2f6332a..81c3c6e4 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap
@@ -7,21 +7,6 @@ pos: 1243
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1655
     ad: 1655
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap
index c9b51277..af3a87fd 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap
@@ -7,21 +7,6 @@ pos: 1438
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 2900
     ad: 2900
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap
index 8d8f87a2..904e7ea2 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap
@@ -7,21 +7,6 @@ pos: 1824
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 1752
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap
index f6c463a6..bfa7b0ca 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap
@@ -7,21 +7,6 @@ pos: 2633
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 2269
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap
index 85705b5b..1568e48f 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap
@@ -7,21 +7,6 @@ pos: 2706
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 2020
     ad: 2020
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap
index 24f0ef6c..e0dca656 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap
@@ -7,21 +7,6 @@ pos: 3010
 reference: G
 alternative: A
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 1685
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap
index d734a796..e99e8bc6 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap
@@ -119,21 +119,6 @@ ann_fields:
     protein_pos: ~
     distance: -794
     messages: ~
-gnomad_exomes_an: 2368
-gnomad_exomes_hom: 10
-gnomad_exomes_het: 80
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -153,3 +138,18 @@ call_info:
     dp: 23
     ad: 11
     phasing_id: ~
+gnomad_exomes_an: 2368
+gnomad_exomes_hom: 10
+gnomad_exomes_het: 80
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap
index 17777f22..c3f7b67e 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap
@@ -7,21 +7,6 @@ pos: 3505
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1664
     ad: 1664
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap
index be13a9fc..6566cd19 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap
@@ -7,21 +7,6 @@ pos: 3784
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/1
@@ -41,3 +26,18 @@ call_info:
     dp: 1991
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap
index 3b4f2f9d..8574d6c9 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap
@@ -7,21 +7,6 @@ pos: 4769
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 2108
     ad: 2108
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap
index 5deca81c..5959b3be 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap
@@ -7,21 +7,6 @@ pos: 5046
 reference: G
 alternative: A
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1661
     ad: 1661
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap
index 71d56608..7d472bfb 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap
@@ -7,21 +7,6 @@ pos: 5460
 reference: G
 alternative: A
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1970
     ad: 1968
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap
index 61bed043..d4d9dd52 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap
@@ -7,21 +7,6 @@ pos: 7028
 reference: C
 alternative: T
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1946
     ad: 1945
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap
index db47d34a..79819260 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap
@@ -7,21 +7,6 @@ pos: 7864
 reference: C
 alternative: T
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 2746
     ad: 2746
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap
index 4db0bcf1..c64b674a 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap
@@ -7,21 +7,6 @@ pos: 8170
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1774
     ad: 1774
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap
index b9d7cd32..1e787feb 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap
@@ -7,21 +7,6 @@ pos: 8251
 reference: G
 alternative: A
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1625
     ad: 1624
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap
index 7f7ea042..334983e8 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap
@@ -7,21 +7,6 @@ pos: 8860
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 2241
     ad: 2241
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap
index 1425d851..43a5f962 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap
@@ -119,21 +119,6 @@ ann_fields:
     protein_pos: ~
     distance: -796
     messages: ~
-gnomad_exomes_an: 3866
-gnomad_exomes_hom: 244
-gnomad_exomes_het: 618
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -153,3 +138,18 @@ call_info:
     dp: 22
     ad: 11
     phasing_id: ~
+gnomad_exomes_an: 3866
+gnomad_exomes_hom: 244
+gnomad_exomes_het: 618
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap
index 114acae2..9203ccc6 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap
@@ -7,21 +7,6 @@ pos: 8994
 reference: G
 alternative: A
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1918
     ad: 1917
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap
index d2d6673d..f3d3be09 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap
@@ -7,21 +7,6 @@ pos: 9007
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 1735
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap
index 3d343365..15091766 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap
@@ -7,21 +7,6 @@ pos: 9150
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 2767
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap
index c92f309c..1a9bf9a1 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap
@@ -7,21 +7,6 @@ pos: 9380
 reference: G
 alternative: A
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 2547
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap
index fe0fc8ec..4522b5a2 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap
@@ -7,21 +7,6 @@ pos: 10097
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1851
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap
index a0b81a19..f20b6f09 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap
@@ -7,21 +7,6 @@ pos: 11204
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 2418
     ad: 2418
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap
index 42f6be42..e60b17f1 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap
@@ -7,21 +7,6 @@ pos: 11674
 reference: C
 alternative: T
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 2180
     ad: 2179
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap
index 2e49a8ca..26e1826a 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap
@@ -7,21 +7,6 @@ pos: 11719
 reference: G
 alternative: A
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 2203
     ad: 2203
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap
index 880f3034..112aaa62 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap
@@ -7,21 +7,6 @@ pos: 11947
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1804
     ad: 1804
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap
index dbefc573..e8a8c2dc 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap
@@ -7,21 +7,6 @@ pos: 12414
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1733
     ad: 1733
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap
index d984ad0e..24837d66 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap
@@ -119,21 +119,6 @@ ann_fields:
     protein_pos: ~
     distance: -798
     messages: ~
-gnomad_exomes_an: 5066
-gnomad_exomes_hom: 546
-gnomad_exomes_het: 795
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/1
@@ -153,3 +138,19 @@ call_info:
     dp: 22
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 5066
+gnomad_exomes_hom: 546
+gnomad_exomes_het: 795
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
+
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap
index 7601069d..05d718ce 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap
@@ -7,21 +7,6 @@ pos: 12648
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1781
     ad: 1777
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap
index a52cb702..e1928baa 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap
@@ -7,21 +7,6 @@ pos: 12705
 reference: C
 alternative: T
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1622
     ad: 1621
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap
index 7b707647..c2fc5416 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap
@@ -7,21 +7,6 @@ pos: 13406
 reference: G
 alternative: A
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1957
     ad: 733
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap
index 0c3acda8..42b81936 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap
@@ -7,21 +7,6 @@ pos: 13611
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 2835
     ad: 2834
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap
index 71e1d605..dce66dd1 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap
@@ -7,21 +7,6 @@ pos: 13928
 reference: G
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1880
     ad: 1880
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap
index c29511b9..264a2925 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap
@@ -7,21 +7,6 @@ pos: 14148
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1962
     ad: 1962
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap
index 83967ff7..261174f8 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap
@@ -7,21 +7,6 @@ pos: 14766
 reference: C
 alternative: T
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 2358
     ad: 2355
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap
index 6ada0254..12916e48 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap
@@ -7,21 +7,6 @@ pos: 15326
 reference: A
 alternative: G
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 2690
     ad: 2690
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap
index 50c77c08..72cf3d51 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap
@@ -7,21 +7,6 @@ pos: 15884
 reference: G
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 2734
     ad: 2733
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap
index b46830b2..21ea363c 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap
@@ -7,21 +7,6 @@ pos: 16184
 reference: C
 alternative: T
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1478
     ad: 1478
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap
index bcb1bf6d..d3c70cf2 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap
@@ -119,21 +119,6 @@ ann_fields:
     protein_pos: ~
     distance: -798
     messages: ~
-gnomad_exomes_an: 4200
-gnomad_exomes_hom: 29
-gnomad_exomes_het: 334
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/1
@@ -153,3 +138,18 @@ call_info:
     dp: 22
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 4200
+gnomad_exomes_hom: 29
+gnomad_exomes_het: 334
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap
index b00b1ebf..36e089af 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap
@@ -7,21 +7,6 @@ pos: 16223
 reference: C
 alternative: T
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1472
     ad: 1472
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap
index 3e9166af..19bf7f0b 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap
@@ -7,21 +7,6 @@ pos: 16263
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 1475
     ad: 0
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap
index 8f0b026e..8dbee52a 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap
@@ -7,21 +7,6 @@ pos: 16292
 reference: C
 alternative: T
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -41,3 +26,18 @@ call_info:
     dp: 1476
     ad: 1476
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap
index b808c18f..e5ffe45e 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap
@@ -7,21 +7,6 @@ pos: 16519
 reference: T
 alternative: C
 ann_fields: []
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -41,3 +26,18 @@ call_info:
     dp: 1744
     ad: 1744
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap
index bf10b080..0865f189 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap
@@ -119,21 +119,6 @@ ann_fields:
     protein_pos: ~
     distance: -800
     messages: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /1/1
@@ -153,3 +138,18 @@ call_info:
     dp: 33
     ad: 11
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap
index 56ef91a1..f2959fc6 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap
@@ -119,21 +119,6 @@ ann_fields:
     protein_pos: ~
     distance: -800
     messages: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -153,3 +138,18 @@ call_info:
     dp: 33
     ad: 21
     phasing_id: ~
+gnomad_exomes_an: 0
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 0
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap
index 0eb11c73..ad7f4bd7 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap
@@ -119,21 +119,6 @@ ann_fields:
     protein_pos: ~
     distance: 1745
     messages: ~
-gnomad_exomes_an: 1936
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 167
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/1
@@ -153,3 +138,18 @@ call_info:
     dp: 35
     ad: 3
     phasing_id: ~
+gnomad_exomes_an: 1936
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 167
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 0
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 0
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf.snap
index 29c4ab48..1d4c5b06 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf.snap
@@ -131,21 +131,6 @@ ann_fields:
       total: 1885
     distance: 44
     messages: ~
-gnomad_exomes_an: 31398
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 56
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 251304
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 369
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
 call_info:
   Case_1_father-N1-DNA1-WGS1:
     genotype: /0/0
@@ -165,3 +150,18 @@ call_info:
     dp: 42
     ad: 21
     phasing_id: ~
+gnomad_exomes_an: 31398
+gnomad_exomes_hom: 0
+gnomad_exomes_het: 56
+gnomad_exomes_hemi: 0
+gnomad_genomes_an: 251304
+gnomad_genomes_hom: 0
+gnomad_genomes_het: 369
+gnomad_genomes_hemi: 0
+helix_an: 0
+helix_hom: 0
+helix_het: 0
+inhouse_an: 0
+inhouse_hom: 0
+inhouse_het: 0
+inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap
index 7b3a05a8..1d9ad79a 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap
@@ -7,6 +7,13 @@ pos: 750
 reference: A
 alternative: G
 ann_fields: []
+call_info:
+  CASE:
+    genotype: /1/1
+    quality: 99
+    dp: 35
+    ad: 35
+    phasing_id: ~
 gnomad_exomes_an: 0
 gnomad_exomes_hom: 0
 gnomad_exomes_het: 0
@@ -22,10 +29,3 @@ inhouse_an: 0
 inhouse_hom: 0
 inhouse_het: 0
 inhouse_hemi: 0
-call_info:
-  CASE:
-    genotype: /1/1
-    quality: 99
-    dp: 35
-    ad: 35
-    phasing_id: ~
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf.snap
index a08c5ac4..1e7c2ff7 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf.snap
@@ -119,6 +119,13 @@ ann_fields:
     protein_pos: ~
     distance: 63
     messages: ~
+call_info:
+  CASE:
+    genotype: "|1|1"
+    quality: 99
+    dp: 80
+    ad: 80
+    phasing_id: 41256074
 gnomad_exomes_an: 20150
 gnomad_exomes_hom: 2725
 gnomad_exomes_het: 5476
@@ -133,11 +140,4 @@ helix_het: 0
 inhouse_an: 0
 inhouse_hom: 0
 inhouse_het: 0
-inhouse_hemi: 0
-call_info:
-  CASE:
-    genotype: "|1|1"
-    quality: 99
-    dp: 80
-    ad: 80
-    phasing_id: 41256074
+inhouse_hemi: 0
\ No newline at end of file

From cd9e4bf06625117428f3d2d4363f3fd72333f18a Mon Sep 17 00:00:00 2001
From: = <=>
Date: Fri, 5 Jul 2024 05:35:57 +0200
Subject: [PATCH 09/23] wip: initial protobuf definition

---
 protos/varfish/v1/query_seqvars.proto | 245 ++++++++++++++++++++++++++
 src/seqvars/query/schema.rs           |   2 +-
 2 files changed, 246 insertions(+), 1 deletion(-)

diff --git a/protos/varfish/v1/query_seqvars.proto b/protos/varfish/v1/query_seqvars.proto
index e69de29b..5cadd748 100644
--- a/protos/varfish/v1/query_seqvars.proto
+++ b/protos/varfish/v1/query_seqvars.proto
@@ -0,0 +1,245 @@
+syntax = "proto3";
+
+package varfish.v1.seqvars;
+
+// Suggestion from emily that might be worth discussing: a few members where I think the enabled bool can be implied by the presence/nonpresence of an optional submessage  making for cleaner code & less branches
+
+
+// Enumeration for recessive mode queries.
+enum RecesssiveMode {
+    Recessive = 0;
+    CompoundRecessive = 1;
+}
+
+// Choices for failing quality thresholds on genotypes.
+enum FailChoice {
+    // Ignore failure
+    Ignore = 0;
+    // Drop whole variant
+    Drop = 1;
+    // TODO COMMENT
+    NoCall = 2;
+}
+
+// Choice for genotype.
+enum GenotypeChoice {
+    // Any genotype
+    Any = 0;
+    // Ref. genotype
+    Ref = 1;
+    // Het. genotype
+    Het = 2;
+    // Hom. genotype
+    Hom = 3;
+    // Non-hom genotype
+    NonHom = 4;
+    // Variant genotype
+    Variant = 5;
+    // Index in comp. het. recessive inheritance
+    ComphetIndex = 6;
+    // Index in recessive inheritance
+    RecessiveIndex = 7;
+    // Parent in recessive inheritance
+    RecessiveParent = 8;
+}
+
+// Quality settings for one sample.
+message QualitySettings {
+    // Minimal coverage for het. sites
+    optional int32 dp_het = 1;
+    // Minimal coverage for hom. sites
+    optional int32 dp_hom = 2;
+    // Minimal genotype quality
+    optional int32 gq = 3;
+    // Minimal allele balance for het. variants
+    optional float ab = 4;
+    // Minimal number of alternate reads
+    optional int32 ad = 5;
+    // Maximal number of alternate reads
+    optional int32 ad_max = 6;
+    // Behaviour on failing quality thresholds
+    FailChoice fail = 7;
+}
+
+message Range {
+    int32 start = 1;
+    int32 end = 2;
+}
+
+message GenomicRegion {
+    // Chromosome
+    string chrom = 1;
+    // Range of region
+    optional Range = 2;
+}
+
+message ClinVarOptions {
+    // Wether to require ClinVar membership
+    bool require_in_clinvar = 1;
+    // Whether to include benign ClinVar variants
+    bool include_benign = 2;
+    // Whether to include pathogenic ClinVar variants
+    bool include_pathogenic = 3;
+    // Whether to include likely benign ClinVar variants
+    bool include_likely_benign = 4;
+    // Whether to include likely pathogenic ClinVar variants
+    bool include_likely_pathogenic = 5;
+    // Whether to include uncertain significance ClinVar variants
+    bool include_uncertain_significance = 6;
+    // Whether to include conflicting interpretation ClinVar variants
+    bool include_conflicting_classifications = 7;
+}
+
+message InhouseFrequencyOptions {
+    // Whether to enable filtration by 1000 Genomes.
+    bool enabled = 1;
+    // Maximal number of in-house carriers
+    optional int32 carriers = 2;
+    // Maximal number of in-house heterozygous carriers
+    optional int32 heterozygous = 3;
+    // Maximal number of in-house homozygous carriers
+    optional int32 homozygous = 4;
+    // Maximal number of in-house hemizygous carriers
+    optional int32 hemizygous = 5;
+}
+
+// TODO: Might be better to structure with an optional submessage instead of all these individual optionals unless they need to be this way for some reason
+
+message GnomadOptions {
+    // Whether to enable filtration by gnomAD exomes
+    bool exomes_enabled = 1;
+    // Whether to enable filtration by gnomAD genomes
+    bool genomes_enabled = 2;
+    // Maximal frequency in gnomAD exomes
+    optional float exomes_frequency = 3;
+    // Maximal number of heterozygous carriers in gnomAD exomes
+    optional int32 exomes_heterozygous = 4;
+    // Maximal number of homozygous carriers in gnomAD exomes
+    optional int32 exomes_homozygous = 5;
+    // Maximal number of hemizygous carriers in gnomAD exomes
+    optional int32 exomes_hemizygous = 6;
+    // Maximal frequency in gnomAD genomes
+    optional float genomes_frequency = 7;
+    // Maximal number of heterozygous carriers in gnomAD genomes
+    optional int32 genomes_heterozygous = 8;
+    // Maximal number of homozygous carriers in gnomAD genomes
+    optional int32 genomes_homozygous = 9;
+    // Maximal number of hemizygous carriers in gnomAD genomes
+    optional int32 genomes_hemizygous = 10;
+}
+
+message HelixMtDbOptions {
+    // Whether to enable filtration by mtDB
+    bool enabled = 1;
+    // Maximal frequency in HelixMtDb
+    optional float frequency = 2;
+    // Maximal number of heterozygous carriers in HelixMtDb
+    optional int32 heteroplasmic = 3;
+    // Maximal number of homozygous carriers in HelixMtDb
+    optional int32 homoplasmic = 4;
+}
+
+message PopulationFrequencyOptions {
+    GnomadOptions gnomad = 1;
+    HelixMtDbOptions helixmtdb = 2;
+}
+
+message VariantTypeOptions {
+    // Whether to include SNVs
+    bool snv = 1;
+    // Whether to include indels
+    bool indel = 2;
+    // Whether to include MNVs
+    bool mnv = 3;
+}
+
+message LocusRelatedOptions {
+    // List of HGNC symbols, HGNC:<ID>s, ENSG<ID>s, or NCBI Gene IDs to restrict the resulting variants to
+    optional repeated  string gene_allowlist = 1;
+    // List of genomic regions to limit restrict the resulting variants to
+    optional repeated GenomicRegion gnomic_region = 2;
+}
+
+message TranscriptOptions {
+    // Whether to include coding transcripts
+    bool transcripts_coding = 1;
+    // Whether to include non-coding transcripts
+    bool transcripts_noncoding = 2;
+    // Maximal distance to next exon, if any
+    optional int32 max_exon_dist = 3;
+}
+
+enum Consequence {
+    // high impact
+    ChromosomeNumberVariation = 0;
+    ExonLossVariant = 1;
+    FrameshiftVariant = 2;
+    RareAminoAcidVariant = 3;
+    SpliceAcceptorVariant = 4;
+    SpliceDonorVariant = 5;
+    StartLost = 6;
+    StopGained = 7;
+    StopLost = 8;
+    TranscriptAblation = 9;
+    // moderate impact
+    ThreePrimeUtrTruncation = 10;
+    FivePrimeUtrTruncaction = 11;
+    ConservativeInframeDeletion = 12;
+    ConservativeInframeInsertion = 13;
+    DisruptiveInframeDeletion = 14;
+    DisruptiveInframeInsertion = 15;
+    MissenseVariant = 16;
+    RegulatoryRegionAblation = 17;
+    SpliceRegionVariant = 18;
+    TbfsAblation = 19;
+    // low impact
+    FivePrimeUtrPrematureStartCodonGainVariant = 20;
+    InitiatorCodonVariant = 21;
+    StartRetained = 22;
+    StopRetainedVariant = 23;
+    SynonymousVariant = 24;
+    // modifier
+    ThreePrimeUtrVariant = 25;
+    FivePrimeUtrVariant = 26;
+    CodingSequenceVariant = 27;
+    ConservedIntergenicVariant = 28;
+    ConservedIntronVariant = 29;
+    DownstreamGeneVariant = 30;
+    ExonVariant = 31;
+    FeatureElongation = 32;
+    FeatureTruncation = 33;
+    GeneVariant = 34;
+    IntergenicVariant = 35;
+    IntronVariant = 36;
+    MatureMirnaVariant = 37;
+    // miRNA
+    Mirna = 38;
+    NmdTranscriptVariant = 39;
+    NonCodingTranscriptExonVariant = 40;
+    NonCodingTranscriptIntronVariant = 41;
+    RegulatoryRegionAmplification = 42;
+    RegulatoryRegionVariant = 43;
+    TfBindingSiteVariant = 44;
+    TfbsAmplification = 45;
+    TranscriptAmplification = 46;
+    TranscriptVariant = 47;
+    UpstreamGeneVariant = 48;
+}
+
+
+message CaseQuery {
+    // Molecular consequences to consider
+    repeated Consequence consequences = 1;
+    // Quality settings for each individual
+    map<string, QualitySettings> quality = 2;
+    // Genotype choice for each individual
+    map<string, GenotypeChoice> genotype = 3;
+    TranscriptOptions transcript = 4;
+    VariantTypeOptions var_type = 5;
+    LocusRelatedOptions locus = 6;
+    // ClinVar related filter options
+    ClinVarOptions clinvar = 7;
+    // PopulationFrequency related filter options
+    PopulationFrequencyOptions population_frequency = 8;
+    InhouseFrequencyOptions inhouse = 9;
+}
\ No newline at end of file
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index cfdf0a20..50c1c9c4 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -314,7 +314,7 @@ pub struct CaseQuery {
     #[serde(flatten)]
     pub locus: LocusRelatedOptions,
 
-    // TODO v moving this into ClinVarOptions without making things meh seems to be annoying
+    // In protobuf this lives inside ClinVarOptions
     /// Wether to require ClinVar membership.
     pub require_in_clinvar: bool,
     /// ClinVar related filter options.

From 81543aab9fd3ce43e8413b9188a1b55291a8745d Mon Sep 17 00:00:00 2001
From: = <=>
Date: Fri, 5 Jul 2024 06:33:41 +0200
Subject: [PATCH 10/23] chore: add proto file to build.rs

---
 build.rs                              |   1 +
 protos/varfish/v1/query_seqvars.proto | 124 +++++++++++++-------------
 src/pbs.rs                            |   4 +
 3 files changed, 68 insertions(+), 61 deletions(-)

diff --git a/build.rs b/build.rs
index cb078b03..8b36e2de 100644
--- a/build.rs
+++ b/build.rs
@@ -9,6 +9,7 @@ fn main() -> Result<(), anyhow::Error> {
         "varfish/v1/clinvar.proto",
         "varfish/v1/sv.proto",
         "varfish/v1/worker.proto",
+        "varfish/v1/query_seqvars.proto"
     ]
     .iter()
     .map(|f| root.join(f))
diff --git a/protos/varfish/v1/query_seqvars.proto b/protos/varfish/v1/query_seqvars.proto
index 5cadd748..7ab704e0 100644
--- a/protos/varfish/v1/query_seqvars.proto
+++ b/protos/varfish/v1/query_seqvars.proto
@@ -5,6 +5,64 @@ package varfish.v1.seqvars;
 // Suggestion from emily that might be worth discussing: a few members where I think the enabled bool can be implied by the presence/nonpresence of an optional submessage  making for cleaner code & less branches
 
 
+
+enum Consequence {
+    // high impact
+    ChromosomeNumberVariation = 0;
+    ExonLossVariant = 1;
+    FrameshiftVariant = 2;
+    RareAminoAcidVariant = 3;
+    SpliceAcceptorVariant = 4;
+    SpliceDonorVariant = 5;
+    StartLost = 6;
+    StopGained = 7;
+    StopLost = 8;
+    TranscriptAblation = 9;
+    // moderate impact
+    ThreePrimeUtrTruncation = 10;
+    FivePrimeUtrTruncaction = 11;
+    ConservativeInframeDeletion = 12;
+    ConservativeInframeInsertion = 13;
+    DisruptiveInframeDeletion = 14;
+    DisruptiveInframeInsertion = 15;
+    MissenseVariant = 16;
+    RegulatoryRegionAblation = 17;
+    SpliceRegionVariant = 18;
+    TbfsAblation = 19;
+    // low impact
+    FivePrimeUtrPrematureStartCodonGainVariant = 20;
+    InitiatorCodonVariant = 21;
+    StartRetained = 22;
+    StopRetainedVariant = 23;
+    SynonymousVariant = 24;
+    // modifier
+    ThreePrimeUtrVariant = 25;
+    FivePrimeUtrVariant = 26;
+    CodingSequenceVariant = 27;
+    ConservedIntergenicVariant = 28;
+    ConservedIntronVariant = 29;
+    DownstreamGeneVariant = 30;
+    ExonVariant = 31;
+    FeatureElongation = 32;
+    FeatureTruncation = 33;
+    GeneVariant = 34;
+    IntergenicVariant = 35;
+    IntronVariant = 36;
+    MatureMirnaVariant = 37;
+    // miRNA
+    Mirna = 38;
+    NmdTranscriptVariant = 39;
+    NonCodingTranscriptExonVariant = 40;
+    NonCodingTranscriptIntronVariant = 41;
+    RegulatoryRegionAmplification = 42;
+    RegulatoryRegionVariant = 43;
+    TfBindingSiteVariant = 44;
+    TfbsAmplification = 45;
+    TranscriptAmplification = 46;
+    TranscriptVariant = 47;
+    UpstreamGeneVariant = 48;
+}
+
 // Enumeration for recessive mode queries.
 enum RecesssiveMode {
     Recessive = 0;
@@ -70,7 +128,7 @@ message GenomicRegion {
     // Chromosome
     string chrom = 1;
     // Range of region
-    optional Range = 2;
+    optional Range range = 2;
 }
 
 message ClinVarOptions {
@@ -153,11 +211,13 @@ message VariantTypeOptions {
     bool mnv = 3;
 }
 
+// TODO: I've taken the liberty of turning the Option<Vec>> into just repeated since protobuf doesn't support it and there appear to be no cases where checking for 0 length wouldn't lead to the same thing
+
 message LocusRelatedOptions {
     // List of HGNC symbols, HGNC:<ID>s, ENSG<ID>s, or NCBI Gene IDs to restrict the resulting variants to
-    optional repeated  string gene_allowlist = 1;
+    repeated string gene_allowlist = 1;
     // List of genomic regions to limit restrict the resulting variants to
-    optional repeated GenomicRegion gnomic_region = 2;
+    repeated GenomicRegion genomic_region = 2;
 }
 
 message TranscriptOptions {
@@ -169,64 +229,6 @@ message TranscriptOptions {
     optional int32 max_exon_dist = 3;
 }
 
-enum Consequence {
-    // high impact
-    ChromosomeNumberVariation = 0;
-    ExonLossVariant = 1;
-    FrameshiftVariant = 2;
-    RareAminoAcidVariant = 3;
-    SpliceAcceptorVariant = 4;
-    SpliceDonorVariant = 5;
-    StartLost = 6;
-    StopGained = 7;
-    StopLost = 8;
-    TranscriptAblation = 9;
-    // moderate impact
-    ThreePrimeUtrTruncation = 10;
-    FivePrimeUtrTruncaction = 11;
-    ConservativeInframeDeletion = 12;
-    ConservativeInframeInsertion = 13;
-    DisruptiveInframeDeletion = 14;
-    DisruptiveInframeInsertion = 15;
-    MissenseVariant = 16;
-    RegulatoryRegionAblation = 17;
-    SpliceRegionVariant = 18;
-    TbfsAblation = 19;
-    // low impact
-    FivePrimeUtrPrematureStartCodonGainVariant = 20;
-    InitiatorCodonVariant = 21;
-    StartRetained = 22;
-    StopRetainedVariant = 23;
-    SynonymousVariant = 24;
-    // modifier
-    ThreePrimeUtrVariant = 25;
-    FivePrimeUtrVariant = 26;
-    CodingSequenceVariant = 27;
-    ConservedIntergenicVariant = 28;
-    ConservedIntronVariant = 29;
-    DownstreamGeneVariant = 30;
-    ExonVariant = 31;
-    FeatureElongation = 32;
-    FeatureTruncation = 33;
-    GeneVariant = 34;
-    IntergenicVariant = 35;
-    IntronVariant = 36;
-    MatureMirnaVariant = 37;
-    // miRNA
-    Mirna = 38;
-    NmdTranscriptVariant = 39;
-    NonCodingTranscriptExonVariant = 40;
-    NonCodingTranscriptIntronVariant = 41;
-    RegulatoryRegionAmplification = 42;
-    RegulatoryRegionVariant = 43;
-    TfBindingSiteVariant = 44;
-    TfbsAmplification = 45;
-    TranscriptAmplification = 46;
-    TranscriptVariant = 47;
-    UpstreamGeneVariant = 48;
-}
-
-
 message CaseQuery {
     // Molecular consequences to consider
     repeated Consequence consequences = 1;
diff --git a/src/pbs.rs b/src/pbs.rs
index af343a85..f58812ca 100644
--- a/src/pbs.rs
+++ b/src/pbs.rs
@@ -6,6 +6,10 @@ pub mod clinvar {
     include!(concat!(env!("OUT_DIR"), "/varfish.v1.clinvar.serde.rs"));
 }
 
+pub mod seqvars {
+    include!(concat!(env!("OUT_DIR"), "/varfish.v1.seqvars.rs"));
+    include!(concat!(env!("OUT_DIR"), "/varfish.v1.seqvars.serde.rs"));}
+
 /// Code generate for protobufs by `prost-build`.
 pub mod svs {
     include!(concat!(env!("OUT_DIR"), "/varfish.v1.svs.rs"));

From a63096bf93b5438ba03e6af5b3783a84aa9008e1 Mon Sep 17 00:00:00 2001
From: = <=>
Date: Sun, 7 Jul 2024 06:01:08 +0200
Subject: [PATCH 11/23] feat: implement conversion from protobuf format into
 legacy format

---
 src/seqvars/query/schema.rs | 197 +++++++++++++++++++++++++++++++++++-
 1 file changed, 196 insertions(+), 1 deletion(-)

diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 50c1c9c4..b052062b 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -1,6 +1,9 @@
 //! Supporting code for seqvar query definition.
 
+use indexmap::IndexMap;
+use mehari::annotate::seqvars::ann;
 use noodles::vcf;
+use strum::IntoEnumIterator;
 
 use crate::common::genotype_to_string;
 
@@ -29,6 +32,7 @@ pub enum RecessiveMode {
     Clone,
     Copy,
     Default,
+    strum::EnumIter,
 )]
 #[serde(rename_all = "kebab-case")]
 pub enum FailChoice {
@@ -55,6 +59,7 @@ pub enum FailChoice {
     Clone,
     Copy,
     Default,
+    strum::EnumIter,
 )]
 #[serde(rename_all = "kebab-case")]
 pub enum GenotypeChoice {
@@ -128,6 +133,20 @@ pub struct QualitySettings {
     pub fail: FailChoice,
 }
 
+impl From<crate::pbs::seqvars::QualitySettings> for QualitySettings {
+    fn from(old: crate::pbs::seqvars::QualitySettings) -> Self {
+        Self {
+            dp_het: old.dp_het,
+            dp_hom: old.dp_hom,
+            gq: old.gq,
+            ab: old.ab,
+            ad: old.ad,
+            ad_max: old.ad_max,
+            fail: FailChoice::iter().nth(old.fail as usize).unwrap(),
+        }
+    }
+}
+
 /// Data structure to hold a range.
 #[derive(
     serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Hash, Debug, Clone,
@@ -139,6 +158,15 @@ pub struct Range {
     pub end: i32,
 }
 
+impl From<crate::pbs::seqvars::Range> for Range {
+    fn from(value: crate::pbs::seqvars::Range) -> Self {
+        Self {
+            start: value.start,
+            end: value.end,
+        }
+    }
+}
+
 /// Data struture to hold a genomic region.
 #[derive(
     serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Hash, Debug, Clone,
@@ -150,6 +178,15 @@ pub struct GenomicRegion {
     pub range: Option<Range>,
 }
 
+impl From<crate::pbs::seqvars::GenomicRegion> for GenomicRegion {
+    fn from(other: crate::pbs::seqvars::GenomicRegion) -> Self {
+        Self {
+            chrom: other.chrom,
+            range: other.range.map(Range::from),
+        }
+    }
+}
+
 serde_with::with_prefix!(prefix_clinvar "clinvar_");
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -168,6 +205,19 @@ pub struct ClinVarOptions {
     pub include_conflicting_classifications: bool,
 }
 
+impl From<crate::pbs::seqvars::ClinVarOptions> for ClinVarOptions {
+    fn from(other: crate::pbs::seqvars::ClinVarOptions) -> Self {
+        Self {
+            include_benign: other.include_benign,
+            include_pathogenic: other.include_pathogenic,
+            include_likely_benign: other.include_likely_benign,
+            include_likely_pathogenic: other.include_likely_pathogenic,
+            include_uncertain_significance: other.include_uncertain_significance,
+            include_conflicting_classifications: other.include_conflicting_classifications,
+        }
+    }
+}
+
 serde_with::with_prefix!(prefix_inhouse "inhouse_");
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -185,6 +235,18 @@ pub struct InhouseFrequencyOptions {
     pub hemizygous: Option<i32>,
 }
 
+impl From<crate::pbs::seqvars::InhouseFrequencyOptions> for InhouseFrequencyOptions {
+    fn from(other: crate::pbs::seqvars::InhouseFrequencyOptions) -> Self {
+        Self {
+            enabled: other.enabled,
+            carriers: other.carriers,
+            heterozygous: other.heterozygous,
+            homozygous: other.homozygous,
+            hemizygous: other.hemizygous,
+        }
+    }
+}
+
 serde_with::with_prefix!(prefix_gnomad "gnomad_");
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -213,6 +275,23 @@ pub struct GnomadOptions {
     pub genomes_hemizygous: Option<i32>,
 }
 
+impl From<crate::pbs::seqvars::GnomadOptions> for GnomadOptions {
+    fn from(other: crate::pbs::seqvars::GnomadOptions) -> Self {
+        Self {
+            exomes_enabled: other.exomes_enabled,
+            genomes_enabled: other.genomes_enabled,
+            exomes_frequency: other.exomes_frequency,
+            exomes_heterozygous: other.exomes_heterozygous,
+            exomes_homozygous: other.exomes_homozygous,
+            exomes_hemizygous: other.exomes_hemizygous,
+            genomes_frequency: other.genomes_frequency,
+            genomes_heterozygous: other.genomes_heterozygous,
+            genomes_homozygous: other.genomes_homozygous,
+            genomes_hemizygous: other.genomes_hemizygous,
+        }
+    }
+}
+
 serde_with::with_prefix!(prefix_helixmtdb "helixmtdb_");
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -228,6 +307,17 @@ pub struct HelixMtDbOptions {
     pub homoplasmic: Option<i32>,
 }
 
+impl From<crate::pbs::seqvars::HelixMtDbOptions> for HelixMtDbOptions {
+    fn from(other: crate::pbs::seqvars::HelixMtDbOptions) -> Self {
+        Self {
+            enabled: other.enabled,
+            frequency: other.frequency,
+            heteroplasmic: other.heteroplasmic,
+            homoplasmic: other.homoplasmic,
+        }
+    }
+}
+
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
 pub struct PopulationFrequencyOptions {
@@ -237,6 +327,21 @@ pub struct PopulationFrequencyOptions {
     pub helixmtdb: HelixMtDbOptions,
 }
 
+impl From<crate::pbs::seqvars::PopulationFrequencyOptions> for PopulationFrequencyOptions {
+    fn from(other: crate::pbs::seqvars::PopulationFrequencyOptions) -> Self {
+        Self {
+            gnomad: other
+                .gnomad
+                .expect("missing field in PopulationFrequencySptions: gnomad")
+                .into(),
+            helixmtdb: other
+                .helixmtdb
+                .expect("missing ield in PopulationFrequencyOptions: helixmtdb")
+                .into(),
+        }
+    }
+}
+
 serde_with::with_prefix!(prefix_var_type "var_type_");
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
 #[serde(default)]
@@ -259,6 +364,16 @@ impl Default for VariantTypeOptions {
     }
 }
 
+impl From<crate::pbs::seqvars::VariantTypeOptions> for VariantTypeOptions {
+    fn from(other: crate::pbs::seqvars::VariantTypeOptions) -> Self {
+        Self {
+            snv: other.snv,
+            indel: other.indel,
+            mnv: other.mnv,
+        }
+    }
+}
+
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
 pub struct LocusRelatedOptions {
@@ -269,6 +384,28 @@ pub struct LocusRelatedOptions {
     pub genomic_regions: Option<Vec<GenomicRegion>>,
 }
 
+impl From<crate::pbs::seqvars::LocusRelatedOptions> for LocusRelatedOptions {
+    fn from(other: crate::pbs::seqvars::LocusRelatedOptions) -> Self {
+        Self {
+            gene_allowlist: match other.gene_allowlist.first() {
+                None => None,
+                _ => Some(other.gene_allowlist),
+            },
+            genomic_regions: match other.genomic_region.first() {
+                None => None,
+                _ => Some(
+                    other
+                        .genomic_region
+                        .iter()
+                        .map(std::borrow::ToOwned::to_owned)
+                        .map(GenomicRegion::from)
+                        .collect(),
+                ),
+            },
+        }
+    }
+}
+
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
 #[serde(default)]
 pub struct TranscriptOptions {
@@ -280,6 +417,16 @@ pub struct TranscriptOptions {
     pub max_exon_dist: Option<i32>,
 }
 
+impl From<crate::pbs::seqvars::TranscriptOptions> for TranscriptOptions {
+    fn from(other: crate::pbs::seqvars::TranscriptOptions) -> Self {
+        Self {
+            transcripts_coding: other.transcripts_coding,
+            transcripts_noncoding: other.transcripts_noncoding,
+            max_exon_dist: other.max_exon_dist,
+        }
+    }
+}
+
 impl Default for TranscriptOptions {
     fn default() -> Self {
         TranscriptOptions {
@@ -299,6 +446,7 @@ pub struct CaseQuery {
 
     /// Quality settings for each individual.
     pub quality: indexmap::IndexMap<String, QualitySettings>,
+
     /// Genotype choice for each individual.
     pub genotype: indexmap::IndexMap<String, Option<GenotypeChoice>>,
 
@@ -330,6 +478,54 @@ pub struct CaseQuery {
     pub inhouse: InhouseFrequencyOptions,
 }
 
+impl From<crate::pbs::seqvars::CaseQuery> for CaseQuery {
+    fn from(other: crate::pbs::seqvars::CaseQuery) -> Self {
+        let consequences: Vec<_> = other
+            .consequences
+            .iter()
+            .map(|x| ann::Consequence::iter().nth(*x as usize).unwrap())
+            .collect();
+        let quality: IndexMap<String, QualitySettings> = other
+            .quality
+            .iter()
+            .map(|(x, y)| (x.to_owned(), y.clone().into()))
+            .collect();
+
+        Self {
+            consequences,
+            quality,
+            genotype: other
+                .genotype
+                .iter()
+                .map(|(x, y)| (x.to_owned(), GenotypeChoice::iter().nth(*y as usize)))
+                .collect(),
+            // Protobuf allows retroactively declaring fields optional so we need to enforce presence here
+            transcript: other
+                .transcript
+                .expect("missing field in CaseQuery: transcript")
+                .into(),
+            var_type: other
+                .var_type
+                .expect("missing field in CaseQuery: var_type")
+                .into(),
+            locus: other
+                .locus
+                .expect("missing field in CaseQuery: locus")
+                .into(),
+            require_in_clinvar: other.clinvar.is_some(),
+            clinvar: other.clinvar.unwrap_or_default().into(),
+            population_frequency: other
+                .population_frequency
+                .expect("Missing field in CaseQuery: population_frequency")
+                .into(),
+            inhouse: other
+                .inhouse
+                .expect("Missing field in CaseQuery: inhouse")
+                .into(),
+        }
+    }
+}
+
 impl Default for ClinVarOptions {
     fn default() -> Self {
         Self {
@@ -431,7 +627,6 @@ pub struct Gnomads {
 
 // Name difference due to legacy json
 serde_with::with_prefix!(prefix_helix "helix_");
-
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
 pub struct HelixMtDBs {
     /// Number of alleles in HelixMtDb cohort (only chrMT).

From 4dbac9f2db78a3626a5e1ed944f7e00b966ebfea Mon Sep 17 00:00:00 2001
From: = <=>
Date: Fri, 19 Jul 2024 08:18:27 +0200
Subject: [PATCH 12/23] implement changes from review. (tests fail, needs
 readjusting on the rust side of things still)

---
 build.rs                                   |   2 +-
 protos/varfish/v1/query_seqvars.proto      | 106 +++++++++---------
 src/pbs.rs                                 |   3 +-
 src/seqvars/query/interpreter/frequency.rs |  82 +++++++-------
 src/seqvars/query/interpreter/quality.rs   |  28 ++---
 src/seqvars/query/schema.rs                | 123 ++++++++++++---------
 6 files changed, 187 insertions(+), 157 deletions(-)

diff --git a/build.rs b/build.rs
index 8b36e2de..cc57b78e 100644
--- a/build.rs
+++ b/build.rs
@@ -9,7 +9,7 @@ fn main() -> Result<(), anyhow::Error> {
         "varfish/v1/clinvar.proto",
         "varfish/v1/sv.proto",
         "varfish/v1/worker.proto",
-        "varfish/v1/query_seqvars.proto"
+        "varfish/v1/query_seqvars.proto",
     ]
     .iter()
     .map(|f| root.join(f))
diff --git a/protos/varfish/v1/query_seqvars.proto b/protos/varfish/v1/query_seqvars.proto
index 7ab704e0..84e9c0a5 100644
--- a/protos/varfish/v1/query_seqvars.proto
+++ b/protos/varfish/v1/query_seqvars.proto
@@ -2,12 +2,10 @@ syntax = "proto3";
 
 package varfish.v1.seqvars;
 
-// Suggestion from emily that might be worth discussing: a few members where I think the enabled bool can be implied by the presence/nonpresence of an optional submessage  making for cleaner code & less branches
-
-
 
+// The Variant consequence
 enum Consequence {
-    // high impact
+    // high impact    
     ChromosomeNumberVariation = 0;
     ExonLossVariant = 1;
     FrameshiftVariant = 2;
@@ -65,18 +63,9 @@ enum Consequence {
 
 // Enumeration for recessive mode queries.
 enum RecesssiveMode {
-    Recessive = 0;
-    CompoundRecessive = 1;
-}
-
-// Choices for failing quality thresholds on genotypes.
-enum FailChoice {
-    // Ignore failure
-    Ignore = 0;
-    // Drop whole variant
-    Drop = 1;
-    // TODO COMMENT
-    NoCall = 2;
+    Unknown = 0;
+    Recessive = 1;
+    CompoundRecessive = 2;
 }
 
 // Choice for genotype.
@@ -102,21 +91,23 @@ enum GenotypeChoice {
 }
 
 // Quality settings for one sample.
-message QualitySettings {
+message SampleQualitySettings {
+    // Name of the sample filtered for
+    string sample = 1;
+    // Enable filter for sample.
+    bool enabled = 2;
     // Minimal coverage for het. sites
-    optional int32 dp_het = 1;
+    optional int32 dp_het = 3;
     // Minimal coverage for hom. sites
-    optional int32 dp_hom = 2;
+    optional int32 dp_hom = 4;
     // Minimal genotype quality
-    optional int32 gq = 3;
+    optional int32 gq = 5;
     // Minimal allele balance for het. variants
-    optional float ab = 4;
+    optional float ab = 6;
     // Minimal number of alternate reads
-    optional int32 ad = 5;
+    optional int32 ad = 7;
     // Maximal number of alternate reads
-    optional int32 ad_max = 6;
-    // Behaviour on failing quality thresholds
-    FailChoice fail = 7;
+    optional int32 ad_max = 8;
 }
 
 message Range {
@@ -148,6 +139,8 @@ message ClinVarOptions {
     bool include_conflicting_classifications = 7;
 }
 
+
+
 message InhouseFrequencyOptions {
     // Whether to enable filtration by 1000 Genomes.
     bool enabled = 1;
@@ -161,29 +154,33 @@ message InhouseFrequencyOptions {
     optional int32 hemizygous = 5;
 }
 
-// TODO: Might be better to structure with an optional submessage instead of all these individual optionals unless they need to be this way for some reason
-
-message GnomadOptions {
-    // Whether to enable filtration by gnomAD exomes
-    bool exomes_enabled = 1;
-    // Whether to enable filtration by gnomAD genomes
-    bool genomes_enabled = 2;
-    // Maximal frequency in gnomAD exomes
-    optional float exomes_frequency = 3;
-    // Maximal number of heterozygous carriers in gnomAD exomes
-    optional int32 exomes_heterozygous = 4;
-    // Maximal number of homozygous carriers in gnomAD exomes
-    optional int32 exomes_homozygous = 5;
-    // Maximal number of hemizygous carriers in gnomAD exomes
-    optional int32 exomes_hemizygous = 6;
-    // Maximal frequency in gnomAD genomes
-    optional float genomes_frequency = 7;
-    // Maximal number of heterozygous carriers in gnomAD genomes
-    optional int32 genomes_heterozygous = 8;
-    // Maximal number of homozygous carriers in gnomAD genomes
-    optional int32 genomes_homozygous = 9;
-    // Maximal number of hemizygous carriers in gnomAD genomes
-    optional int32 genomes_hemizygous = 10;
+message GnomadNuclearOptions {
+    // Whether to enable filtration by 1000 Genomes.
+    bool enabled = 1;
+    // Maximal number of in-house carriers
+    optional int32 carriers = 2;
+    // Maximal number of in-house heterozygous carriers
+    optional int32 heterozygous = 3;
+    // Maximal number of in-house homozygous carriers
+    optional int32 homozygous = 4;
+    // Maximal number of in-house hemizygous carriers
+    optional int32 hemizygous = 5;
+    // Maximal allele frequency.
+    optional float allele_frequency = 6;
+}
+
+
+message GnomadMitochondrialOptions {
+    // Whether to enable filtration by 1000 Genomes.
+    bool enabled = 1;
+    // Maximal number of carriers
+    optional int32 carriers = 2;
+    // Maximal number of heteroplasmic carriers.
+    optional int32 heteroplasmic = 3;
+    // Maximal number of homoplasmic carriers.
+    optional int32 homoplasmic = 4;
+    // Maximal allele frequency.
+    optional float allele_frequency = 5;
 }
 
 message HelixMtDbOptions {
@@ -198,8 +195,14 @@ message HelixMtDbOptions {
 }
 
 message PopulationFrequencyOptions {
-    GnomadOptions gnomad = 1;
-    HelixMtDbOptions helixmtdb = 2;
+    // gnomAD-exomes filter
+    GnomadNuclearOptions gnomad_exomes = 1;
+    // gnomAD-genomes filter
+    GnomadNuclearOptions gnomad_genomes = 2;
+    // gnomAD-MT filter
+    GnomadMitochondrialOptions gnomad_mt = 3;
+    // HelixMtDb filter
+    HelixMtDbOptions helixmtdb = 4;
 }
 
 message VariantTypeOptions {
@@ -233,13 +236,14 @@ message CaseQuery {
     // Molecular consequences to consider
     repeated Consequence consequences = 1;
     // Quality settings for each individual
-    map<string, QualitySettings> quality = 2;
+    map<string, SampleQualitySettings> quality = 2;
     // Genotype choice for each individual
     map<string, GenotypeChoice> genotype = 3;
     TranscriptOptions transcript = 4;
     VariantTypeOptions var_type = 5;
     LocusRelatedOptions locus = 6;
     // ClinVar related filter options
+    // need to explicitly have an enable function
     ClinVarOptions clinvar = 7;
     // PopulationFrequency related filter options
     PopulationFrequencyOptions population_frequency = 8;
diff --git a/src/pbs.rs b/src/pbs.rs
index f58812ca..a86c866f 100644
--- a/src/pbs.rs
+++ b/src/pbs.rs
@@ -8,7 +8,8 @@ pub mod clinvar {
 
 pub mod seqvars {
     include!(concat!(env!("OUT_DIR"), "/varfish.v1.seqvars.rs"));
-    include!(concat!(env!("OUT_DIR"), "/varfish.v1.seqvars.serde.rs"));}
+    include!(concat!(env!("OUT_DIR"), "/varfish.v1.seqvars.serde.rs"));
+}
 
 /// Code generate for protobufs by `prost-build`.
 pub mod svs {
diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs
index 52fb9849..3131ab76 100644
--- a/src/seqvars/query/interpreter/frequency.rs
+++ b/src/seqvars/query/interpreter/frequency.rs
@@ -23,45 +23,45 @@ pub fn passes(query: &CaseQuery, s: &SequenceVariant) -> Result<bool, anyhow::Er
             );
             return Ok(false);
         }
-    } else if pop.gnomad.exomes_enabled
-        && (pop.gnomad.exomes_frequency.is_some()
-            && s.gnomad_exomes_af() > pop.gnomad.exomes_frequency.expect("tested before")
-            || pop.gnomad.exomes_heterozygous.is_some()
+    } else if pop.gnomad_exomes.enabled
+        && (pop.gnomad_exomes.allele_frequency.is_some()
+            && s.gnomad_exomes_af() > pop.gnomad_exomes.allele_frequency.expect("tested before")
+            || pop.gnomad_exomes.heterozygous.is_some()
                 && s.population_frequencies.gnomad.exomes_het
-                    > pop.gnomad.exomes_heterozygous.expect("tested before")
-            || pop.gnomad.exomes_homozygous.is_some()
+                    > pop.gnomad_exomes.heterozygous.expect("tested before")
+            || pop.gnomad_exomes.homozygous.is_some()
                 && s.population_frequencies.gnomad.exomes_hom
-                    > pop.gnomad.exomes_homozygous.expect("tested before")
-            || pop.gnomad.exomes_hemizygous.is_some()
+                    > pop.gnomad_exomes.homozygous.expect("tested before")
+            || pop.gnomad_exomes.hemizygous.is_some()
                 && s.population_frequencies.gnomad.exomes_hemi
-                    > pop.gnomad.exomes_hemizygous.expect("tested before"))
+                    > pop.gnomad_exomes.hemizygous.expect("tested before"))
     {
         tracing::trace!(
             "variant {:?} fails gnomAD exomes frequency filter {:?}",
             s,
-            &pop.gnomad.exomes_frequency
+            &pop.gnomad_exomes.allele_frequency
         );
         return Ok(false);
     }
 
-    if pop.gnomad.genomes_enabled
-        && (pop.gnomad.genomes_frequency.is_some()
-            && s.gnomad_genomes_af() > pop.gnomad.genomes_frequency.expect("tested before")
-            || pop.gnomad.genomes_heterozygous.is_some()
+    if pop.gnomad_genomes.enabled
+        && (pop.gnomad_genomes.allele_frequency.is_some()
+            && s.gnomad_genomes_af() > pop.gnomad_genomes.allele_frequency.expect("tested before")
+            || pop.gnomad_genomes.heterozygous.is_some()
                 && s.population_frequencies.gnomad.genomes_het
-                    > pop.gnomad.genomes_heterozygous.expect("tested before")
-            || pop.gnomad.genomes_homozygous.is_some()
+                    > pop.gnomad_genomes.heterozygous.expect("tested before")
+            || pop.gnomad_genomes.homozygous.is_some()
                 && s.population_frequencies.gnomad.genomes_hom
-                    > pop.gnomad.genomes_homozygous.expect("tested before")
+                    > pop.gnomad_genomes.homozygous.expect("tested before")
             || !is_mtdna
-                && pop.gnomad.genomes_hemizygous.is_some()
+                && pop.gnomad_genomes.hemizygous.is_some()
                 && s.population_frequencies.gnomad.genomes_hemi
-                    > pop.gnomad.genomes_hemizygous.expect("tested before"))
+                    > pop.gnomad_genomes.hemizygous.expect("tested before"))
     {
         tracing::trace!(
-            "variant {:?} fails gnomAD genomes frequency filter {:?}",
+            "variant {:?} fails gnomAD genomes allele_frequency filter {:?}",
             s,
-            &pop.gnomad.genomes_frequency
+            &pop.gnomad_genomes.allele_frequency
         );
         return Ok(false);
     }
@@ -145,17 +145,17 @@ mod test {
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
         use crate::seqvars::query::schema::{
-            GnomadOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
+            GnomadNuclearOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
         };
 
         let query = CaseQuery {
             population_frequency: PopulationFrequencyOptions {
-                gnomad: GnomadOptions {
-                    exomes_enabled: query_gnomad_exomes_enabled,
-                    exomes_frequency: query_gnomad_exomes_frequency,
-                    exomes_heterozygous: query_gnomad_exomes_heterozygous,
-                    exomes_homozygous: query_gnomad_exomes_homozygous,
-                    exomes_hemizygous: query_gnomad_exomes_hemizygous,
+                gnomad_exomes: GnomadNuclearOptions {
+                    enabled: query_gnomad_exomes_enabled,
+                    allele_frequency: query_gnomad_exomes_frequency,
+                    heterozygous: query_gnomad_exomes_heterozygous,
+                    homozygous: query_gnomad_exomes_homozygous,
+                    hemizygous: query_gnomad_exomes_hemizygous,
                     ..Default::default()
                 },
                 ..Default::default()
@@ -272,17 +272,17 @@ mod test {
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
         use crate::seqvars::query::schema::{
-            GnomadOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
+            GnomadNuclearOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
         };
 
         let query = CaseQuery {
             population_frequency: PopulationFrequencyOptions {
-                gnomad: GnomadOptions {
-                    genomes_enabled: query_gnomad_genomes_enabled,
-                    genomes_frequency: query_gnomad_genomes_frequency,
-                    genomes_heterozygous: query_gnomad_genomes_heterozygous,
-                    genomes_homozygous: query_gnomad_genomes_homozygous,
-                    genomes_hemizygous: query_gnomad_genomes_hemizygous,
+                gnomad_genomes: GnomadNuclearOptions {
+                    enabled: query_gnomad_genomes_enabled,
+                    allele_frequency: query_gnomad_genomes_frequency,
+                    heterozygous: query_gnomad_genomes_heterozygous,
+                    homozygous: query_gnomad_genomes_homozygous,
+                    hemizygous: query_gnomad_genomes_hemizygous,
                     ..Default::default()
                 },
                 ..Default::default()
@@ -483,16 +483,16 @@ mod test {
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
         use crate::seqvars::query::schema::{
-            GnomadOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
+            GnomadNuclearOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
         };
 
         let query = CaseQuery {
             population_frequency: PopulationFrequencyOptions {
-                gnomad: GnomadOptions {
-                    genomes_enabled: query_gnomad_genomes_enabled,
-                    genomes_frequency: query_gnomad_genomes_frequency,
-                    genomes_heterozygous: query_gnomad_genomes_heteroplasmic,
-                    genomes_homozygous: query_gnomad_genomes_homoplasmic,
+                gnomad_genomes: GnomadNuclearOptions {
+                    enabled: query_gnomad_genomes_enabled,
+                    allele_frequency: query_gnomad_genomes_frequency,
+                    heterozygous: query_gnomad_genomes_heteroplasmic,
+                    homozygous: query_gnomad_genomes_homoplasmic,
                     ..Default::default()
                 },
                 ..Default::default()
diff --git a/src/seqvars/query/interpreter/quality.rs b/src/seqvars/query/interpreter/quality.rs
index c77b0b5d..71b51097 100644
--- a/src/seqvars/query/interpreter/quality.rs
+++ b/src/seqvars/query/interpreter/quality.rs
@@ -1,6 +1,8 @@
 use crate::{
     common::strip_gt_leading_slash,
-    seqvars::query::schema::{CallInfo, CaseQuery, FailChoice, QualitySettings, SequenceVariant},
+    seqvars::query::schema::{
+        CallInfo, CaseQuery, FailChoice, SampleQualitySettings, SequenceVariant,
+    },
 };
 
 /// Return type for the `passes` function.
@@ -60,7 +62,7 @@ pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result<PassOrNoCal
 
 /// Return failure code (or None for all-pass) for one sample's call info.
 fn passes_for_sample(
-    quality_settings: &QualitySettings,
+    quality_settings: &SampleQualitySettings,
     call_info: &CallInfo,
 ) -> Option<FailChoice> {
     #[derive(PartialEq, Eq)]
@@ -90,7 +92,7 @@ fn passes_for_sample(
             if let Some(dp_het) = quality_settings.dp_het {
                 if let Some(dp) = call_info.dp {
                     if dp < dp_het {
-                        return Some(quality_settings.fail);
+                        return Some(FailChoice::Ignore); //TODO: Emily Some(quality_settings.fail);
                     }
                 }
             }
@@ -103,7 +105,7 @@ fn passes_for_sample(
                 let ab = if ab_raw > 0.5 { 1.0 - ab_raw } else { ab_raw };
                 let eps = 1e-6f64;
                 if ab + eps < settings_ab as f64 {
-                    return Some(quality_settings.fail);
+                    return Some(FailChoice::Ignore); // TODO: Emily Some(quality_settings.fail);
                 }
             }
         }
@@ -111,7 +113,7 @@ fn passes_for_sample(
             if let Some(dp_hom) = quality_settings.dp_hom {
                 if let Some(dp) = call_info.dp {
                     if dp < dp_hom {
-                        return Some(quality_settings.fail);
+                        return Some(FailChoice::Ignore); // TODO: Emily Some(quality_settings.fail);
                     }
                 }
             }
@@ -122,7 +124,7 @@ fn passes_for_sample(
     // gq
     if let (Some(settings_gq), Some(call_gq)) = (quality_settings.gq, call_info.quality) {
         if call_gq < settings_gq as f32 {
-            return Some(quality_settings.fail);
+            return Some(FailChoice::Ignore); // TODO: Emily Some(quality_settings.fail);
         }
     }
 
@@ -130,14 +132,14 @@ fn passes_for_sample(
         // ad
         if let (Some(settings_ad), Some(call_ad)) = (quality_settings.ad, call_info.ad) {
             if call_ad < settings_ad {
-                return Some(quality_settings.fail);
+                return Some(FailChoice::Ignore); // TODO: Emily Some(quality_settings.fail);
             }
         }
 
         // ad_max
         if let (Some(settings_ad_max), Some(call_ad)) = (quality_settings.ad_max, call_info.ad) {
             if call_ad > settings_ad_max {
-                return Some(quality_settings.fail);
+                return Some(FailChoice::Ignore); // TODO: Emily Some(quality_settings.fail);
             }
         }
     }
@@ -152,7 +154,7 @@ mod test {
     use crate::seqvars::query::schema::{
         CallInfo, CaseQuery,
         FailChoice::{self, *},
-        QualitySettings, SequenceVariant,
+        SampleQualitySettings, SequenceVariant,
     };
 
     #[rstest]
@@ -171,14 +173,14 @@ mod test {
         let query = CaseQuery {
             quality: vec![(
                 String::from("sample"),
-                QualitySettings {
+                SampleQualitySettings {
                     dp_het: None,
                     dp_hom: None,
                     gq: if should_pass { None } else { Some(40) },
                     ab: None,
                     ad: None,
                     ad_max: None,
-                    fail: q_fail,
+                    //TODO: emily fail: q_fail,
                 },
             )]
             .into_iter()
@@ -475,14 +477,14 @@ mod test {
         #[case] c_ad: Option<i32>,
         #[case] expected: Option<FailChoice>,
     ) -> Result<(), anyhow::Error> {
-        let settings = QualitySettings {
+        let settings = SampleQualitySettings {
             dp_het: q_dp_het,
             dp_hom: q_dp_hom,
             gq: q_gq,
             ab: q_ab,
             ad: q_ad,
             ad_max: q_ad_max,
-            fail: q_fail,
+            //TODO: emily fail: q_fail,
         };
         let call_info = CallInfo {
             genotype: c_genotype.map(|s| s.to_string()),
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index b052062b..3f19ded8 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -116,7 +116,7 @@ impl GenotypeChoice {
 
 /// Quality settings for one sample.
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
-pub struct QualitySettings {
+pub struct SampleQualitySettings {
     /// Minimal coverage for het. sites.
     pub dp_het: Option<i32>,
     /// Minimal coverage for hom. sites.
@@ -129,12 +129,10 @@ pub struct QualitySettings {
     pub ad: Option<i32>,
     /// Maximal number of alternate reads
     pub ad_max: Option<i32>,
-    /// Behaviour on failing quality thresholds.
-    pub fail: FailChoice,
 }
 
-impl From<crate::pbs::seqvars::QualitySettings> for QualitySettings {
-    fn from(old: crate::pbs::seqvars::QualitySettings) -> Self {
+impl From<crate::pbs::seqvars::SampleQualitySettings> for SampleQualitySettings {
+    fn from(old: crate::pbs::seqvars::SampleQualitySettings) -> Self {
         Self {
             dp_het: old.dp_het,
             dp_hom: old.dp_hom,
@@ -142,7 +140,7 @@ impl From<crate::pbs::seqvars::QualitySettings> for QualitySettings {
             ab: old.ab,
             ad: old.ad,
             ad_max: old.ad_max,
-            fail: FailChoice::iter().nth(old.fail as usize).unwrap(),
+            //fail: FailChoice::iter().nth(old.fail as usize).unwrap(),
         }
     }
 }
@@ -221,8 +219,23 @@ impl From<crate::pbs::seqvars::ClinVarOptions> for ClinVarOptions {
 serde_with::with_prefix!(prefix_inhouse "inhouse_");
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
-/// TODO: currently unused?
 pub struct InhouseFrequencyOptions {
+    /// Whether to enable filtration by 1000 Genomes.
+    pub enabled: bool,
+    /// Maximal number of in-house carriers
+    pub carriers: Option<i32>,
+    /// Maximal number of in-house heterozygous carriers
+    pub heterozygous: Option<i32>,
+    /// Maximal number of in-house homozygous carriers
+    pub homozygous: Option<i32>,
+    /// Maximal number of in-house hemizygous carriers
+    pub hemizygous: Option<i32>,
+}
+
+#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
+#[serde(default)]
+/// TODO: currently unused?
+pub struct GnomadNuclearOptions {
     /// Whether to enable filtration by 1000 Genomes.
     pub enabled: bool,
     /// Maximal number of in-house carriers.
@@ -233,6 +246,21 @@ pub struct InhouseFrequencyOptions {
     pub homozygous: Option<i32>,
     /// Maximal number of in-house hemizygous carriers.
     pub hemizygous: Option<i32>,
+    // Maximal allele frequency.
+    pub allele_frequency: Option<f32>,
+}
+
+impl From<crate::pbs::seqvars::GnomadNuclearOptions> for GnomadNuclearOptions {
+    fn from(other: crate::pbs::seqvars::GnomadNuclearOptions) -> Self {
+        Self {
+            enabled: other.enabled,
+            carriers: other.carriers,
+            heterozygous: other.heterozygous,
+            homozygous: other.homozygous,
+            hemizygous: other.hemizygous,
+            allele_frequency: other.allele_frequency,
+        }
+    }
 }
 
 impl From<crate::pbs::seqvars::InhouseFrequencyOptions> for InhouseFrequencyOptions {
@@ -250,44 +278,27 @@ impl From<crate::pbs::seqvars::InhouseFrequencyOptions> for InhouseFrequencyOpti
 serde_with::with_prefix!(prefix_gnomad "gnomad_");
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
-pub struct GnomadOptions {
-    /// Whether to enable filtration by gnomAD exomes.
-    pub exomes_enabled: bool,
-    /// Whether to enable filtration by gnomAD genomes
-    pub genomes_enabled: bool,
-
-    /// Maximal frequency in gnomAD exomes.
-    pub exomes_frequency: Option<f32>,
-    /// Maximal number of heterozygous carriers in gnomAD exomes.
-    pub exomes_heterozygous: Option<i32>,
-    /// Maximal number of homozygous carriers in gnomAD exomes.
-    pub exomes_homozygous: Option<i32>,
-    /// Maximal number of hemizygous carriers in gnomAD exomes.
-    pub exomes_hemizygous: Option<i32>,
-
-    /// Maximal frequency in gnomAD genomes.
-    pub genomes_frequency: Option<f32>,
-    /// Maximal number of heterozygous carriers in gnomAD genomes.
-    pub genomes_heterozygous: Option<i32>,
-    /// Maximal number of homozygous carriers in gnomAD genomes.
-    pub genomes_homozygous: Option<i32>,
-    /// Maximal number of hemizygous carriers in gnomAD genomes.
-    pub genomes_hemizygous: Option<i32>,
-}
-
-impl From<crate::pbs::seqvars::GnomadOptions> for GnomadOptions {
-    fn from(other: crate::pbs::seqvars::GnomadOptions) -> Self {
+pub struct GnomadMitochondrialOptions {
+    /// Whether to enable filtration by 1000 Genomes.
+    pub enabled: bool,
+    /// Maximal number of carriers
+    pub carriers: Option<i32>,
+    /// Maximal number of heteroplasmic carriers.
+    pub heteroplasmic: Option<i32>,
+    /// Maximal number of homoplasmic carriers.
+    pub homoplasmic: Option<i32>,
+    /// Maximal allele frequency.
+    pub allele_frequency: Option<f32>,
+}
+
+impl From<crate::pbs::seqvars::GnomadMitochondrialOptions> for GnomadMitochondrialOptions {
+    fn from(other: crate::pbs::seqvars::GnomadMitochondrialOptions) -> Self {
         Self {
-            exomes_enabled: other.exomes_enabled,
-            genomes_enabled: other.genomes_enabled,
-            exomes_frequency: other.exomes_frequency,
-            exomes_heterozygous: other.exomes_heterozygous,
-            exomes_homozygous: other.exomes_homozygous,
-            exomes_hemizygous: other.exomes_hemizygous,
-            genomes_frequency: other.genomes_frequency,
-            genomes_heterozygous: other.genomes_heterozygous,
-            genomes_homozygous: other.genomes_homozygous,
-            genomes_hemizygous: other.genomes_hemizygous,
+            enabled: other.enabled,
+            carriers: other.carriers,
+            heteroplasmic: other.heteroplasmic,
+            homoplasmic: other.homoplasmic,
+            allele_frequency: other.allele_frequency,
         }
     }
 }
@@ -322,7 +333,11 @@ impl From<crate::pbs::seqvars::HelixMtDbOptions> for HelixMtDbOptions {
 #[serde(default)]
 pub struct PopulationFrequencyOptions {
     #[serde(flatten, with = "prefix_gnomad")]
-    pub gnomad: GnomadOptions,
+    pub gnomad_exomes: GnomadNuclearOptions,
+    // TODO emily: flatten right
+    pub gnomad_genomes: GnomadNuclearOptions,
+    // gnomAD-MT filter
+    pub gnomad_mt: GnomadMitochondrialOptions,
     #[serde(flatten, with = "prefix_helixmtdb")]
     pub helixmtdb: HelixMtDbOptions,
 }
@@ -330,9 +345,17 @@ pub struct PopulationFrequencyOptions {
 impl From<crate::pbs::seqvars::PopulationFrequencyOptions> for PopulationFrequencyOptions {
     fn from(other: crate::pbs::seqvars::PopulationFrequencyOptions) -> Self {
         Self {
-            gnomad: other
-                .gnomad
-                .expect("missing field in PopulationFrequencySptions: gnomad")
+            gnomad_exomes: other
+                .gnomad_exomes
+                .expect("missing field in PopulationFrequencyOptions: gnomad_exomes")
+                .into(),
+            gnomad_genomes: other
+                .gnomad_genomes
+                .expect("missing field in PopulationFrequencyOptions: gnomad_genomes")
+                .into(),
+            gnomad_mt: other
+                .gnomad_mt
+                .expect("missing field in PopulationFrequencyOptions: gnomad_mt")
                 .into(),
             helixmtdb: other
                 .helixmtdb
@@ -445,7 +468,7 @@ pub struct CaseQuery {
     pub consequences: Vec<mehari::annotate::seqvars::ann::Consequence>,
 
     /// Quality settings for each individual.
-    pub quality: indexmap::IndexMap<String, QualitySettings>,
+    pub quality: indexmap::IndexMap<String, SampleQualitySettings>,
 
     /// Genotype choice for each individual.
     pub genotype: indexmap::IndexMap<String, Option<GenotypeChoice>>,
@@ -485,7 +508,7 @@ impl From<crate::pbs::seqvars::CaseQuery> for CaseQuery {
             .iter()
             .map(|x| ann::Consequence::iter().nth(*x as usize).unwrap())
             .collect();
-        let quality: IndexMap<String, QualitySettings> = other
+        let quality: IndexMap<String, SampleQualitySettings> = other
             .quality
             .iter()
             .map(|(x, y)| (x.to_owned(), y.clone().into()))

From 402d10d98aa9106734db16fcbecd3a193ded24fd Mon Sep 17 00:00:00 2001
From: = <=>
Date: Fri, 19 Jul 2024 08:58:47 +0200
Subject: [PATCH 13/23] adjust json schema to be closer to original schema

---
 src/seqvars/query/interpreter/quality.rs | 12 ++++++------
 src/seqvars/query/schema.rs              | 13 +++++++++++--
 2 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/src/seqvars/query/interpreter/quality.rs b/src/seqvars/query/interpreter/quality.rs
index 71b51097..3870918f 100644
--- a/src/seqvars/query/interpreter/quality.rs
+++ b/src/seqvars/query/interpreter/quality.rs
@@ -92,7 +92,7 @@ fn passes_for_sample(
             if let Some(dp_het) = quality_settings.dp_het {
                 if let Some(dp) = call_info.dp {
                     if dp < dp_het {
-                        return Some(FailChoice::Ignore); //TODO: Emily Some(quality_settings.fail);
+                        return Some(FailChoice::Drop); //TODO: Emily Some(quality_settings.fail);
                     }
                 }
             }
@@ -105,7 +105,7 @@ fn passes_for_sample(
                 let ab = if ab_raw > 0.5 { 1.0 - ab_raw } else { ab_raw };
                 let eps = 1e-6f64;
                 if ab + eps < settings_ab as f64 {
-                    return Some(FailChoice::Ignore); // TODO: Emily Some(quality_settings.fail);
+                    return Some(FailChoice::Drop); // TODO: Emily Some(quality_settings.fail);
                 }
             }
         }
@@ -113,7 +113,7 @@ fn passes_for_sample(
             if let Some(dp_hom) = quality_settings.dp_hom {
                 if let Some(dp) = call_info.dp {
                     if dp < dp_hom {
-                        return Some(FailChoice::Ignore); // TODO: Emily Some(quality_settings.fail);
+                        return Some(FailChoice::Drop); // TODO: Emily Some(quality_settings.fail);
                     }
                 }
             }
@@ -124,7 +124,7 @@ fn passes_for_sample(
     // gq
     if let (Some(settings_gq), Some(call_gq)) = (quality_settings.gq, call_info.quality) {
         if call_gq < settings_gq as f32 {
-            return Some(FailChoice::Ignore); // TODO: Emily Some(quality_settings.fail);
+            return Some(FailChoice::Drop); // TODO: Emily Some(quality_settings.fail);
         }
     }
 
@@ -132,14 +132,14 @@ fn passes_for_sample(
         // ad
         if let (Some(settings_ad), Some(call_ad)) = (quality_settings.ad, call_info.ad) {
             if call_ad < settings_ad {
-                return Some(FailChoice::Ignore); // TODO: Emily Some(quality_settings.fail);
+                return Some(FailChoice::Drop); // TODO: Emily Some(quality_settings.fail);
             }
         }
 
         // ad_max
         if let (Some(settings_ad_max), Some(call_ad)) = (quality_settings.ad_max, call_info.ad) {
             if call_ad > settings_ad_max {
-                return Some(FailChoice::Ignore); // TODO: Emily Some(quality_settings.fail);
+                return Some(FailChoice::Drop); // TODO: Emily Some(quality_settings.fail);
             }
         }
     }
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 3f19ded8..5799e2e0 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -247,6 +247,7 @@ pub struct GnomadNuclearOptions {
     /// Maximal number of in-house hemizygous carriers.
     pub hemizygous: Option<i32>,
     // Maximal allele frequency.
+    #[serde(rename = "frequency")]
     pub allele_frequency: Option<f32>,
 }
 
@@ -275,7 +276,6 @@ impl From<crate::pbs::seqvars::InhouseFrequencyOptions> for InhouseFrequencyOpti
     }
 }
 
-serde_with::with_prefix!(prefix_gnomad "gnomad_");
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
 pub struct GnomadMitochondrialOptions {
@@ -288,6 +288,7 @@ pub struct GnomadMitochondrialOptions {
     /// Maximal number of homoplasmic carriers.
     pub homoplasmic: Option<i32>,
     /// Maximal allele frequency.
+    #[serde(rename = "frequency")]
     pub allele_frequency: Option<f32>,
 }
 
@@ -329,14 +330,20 @@ impl From<crate::pbs::seqvars::HelixMtDbOptions> for HelixMtDbOptions {
     }
 }
 
+
+serde_with::with_prefix!(prefix_gnomad_exomes "gnomad_exomes_");
+serde_with::with_prefix!(prefix_gnomad_genomes "gnomad_genomes_");
+serde_with::with_prefix!(prefix_gnomad_mt "gnomat_mt_");
 #[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
 #[serde(default)]
 pub struct PopulationFrequencyOptions {
-    #[serde(flatten, with = "prefix_gnomad")]
+    #[serde(flatten, with = "prefix_gnomad_exomes")]
     pub gnomad_exomes: GnomadNuclearOptions,
     // TODO emily: flatten right
+    #[serde(flatten, with = "prefix_gnomad_genomes")]
     pub gnomad_genomes: GnomadNuclearOptions,
     // gnomAD-MT filter
+    #[serde(flatten, with = "prefix_gnomad_mt")]
     pub gnomad_mt: GnomadMitochondrialOptions,
     #[serde(flatten, with = "prefix_helixmtdb")]
     pub helixmtdb: HelixMtDbOptions,
@@ -660,6 +667,8 @@ pub struct HelixMtDBs {
     pub het: i32,
 }
 
+
+serde_with::with_prefix!(prefix_gnomad "gnomad_"); 
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
 
 pub struct PopulationFrequencies {

From 0c07d1ff9482fbd1efec0d868a5b74331bebef07 Mon Sep 17 00:00:00 2001
From: = <=>
Date: Wed, 24 Jul 2024 07:52:47 +0200
Subject: [PATCH 14/23] should be final protobuf schema, tests pass again

---
 protos/varfish/v1/query_seqvars.proto         | 20 ++---
 src/seqvars/query/interpreter/quality.rs      | 39 ++++-----
 src/seqvars/query/mod.rs                      |  2 +-
 src/seqvars/query/schema.rs                   | 79 ++++++++-----------
 ...ema__test__smoke_test_load@empty.json.snap | 13 ++-
 ...hema__test__smoke_test_load@full.json.snap | 15 +++-
 ...test__smoke_test_load@with_extra.json.snap | 15 +++-
 tests/seqvars/query/Case_1.query.json         |  6 +-
 tests/seqvars/query/Case_1.query.json.bak     |  6 +-
 tests/seqvars/query/dragen.query.json         |  2 +-
 tests/seqvars/query/full.json                 |  2 +-
 tests/seqvars/query/with_extra.json           |  2 +-
 12 files changed, 104 insertions(+), 97 deletions(-)

diff --git a/protos/varfish/v1/query_seqvars.proto b/protos/varfish/v1/query_seqvars.proto
index 84e9c0a5..3c7cd3a5 100644
--- a/protos/varfish/v1/query_seqvars.proto
+++ b/protos/varfish/v1/query_seqvars.proto
@@ -92,22 +92,24 @@ enum GenotypeChoice {
 
 // Quality settings for one sample.
 message SampleQualitySettings {
+    // Drop whole variant on failure
+    bool filter_active = 1;
     // Name of the sample filtered for
-    string sample = 1;
+    string sample = 2;
     // Enable filter for sample.
-    bool enabled = 2;
+    bool enabled = 3;
     // Minimal coverage for het. sites
-    optional int32 dp_het = 3;
+    optional int32 dp_het = 4;
     // Minimal coverage for hom. sites
-    optional int32 dp_hom = 4;
+    optional int32 dp_hom = 5;
     // Minimal genotype quality
-    optional int32 gq = 5;
+    optional int32 gq = 6;
     // Minimal allele balance for het. variants
-    optional float ab = 6;
+    optional float ab = 7;
     // Minimal number of alternate reads
-    optional int32 ad = 7;
+    optional int32 ad = 8;
     // Maximal number of alternate reads
-    optional int32 ad_max = 8;
+    optional int32 ad_max = 9;
 }
 
 message Range {
@@ -214,8 +216,6 @@ message VariantTypeOptions {
     bool mnv = 3;
 }
 
-// TODO: I've taken the liberty of turning the Option<Vec>> into just repeated since protobuf doesn't support it and there appear to be no cases where checking for 0 length wouldn't lead to the same thing
-
 message LocusRelatedOptions {
     // List of HGNC symbols, HGNC:<ID>s, ENSG<ID>s, or NCBI Gene IDs to restrict the resulting variants to
     repeated string gene_allowlist = 1;
diff --git a/src/seqvars/query/interpreter/quality.rs b/src/seqvars/query/interpreter/quality.rs
index 3870918f..93a26c2e 100644
--- a/src/seqvars/query/interpreter/quality.rs
+++ b/src/seqvars/query/interpreter/quality.rs
@@ -1,7 +1,7 @@
 use crate::{
     common::strip_gt_leading_slash,
     seqvars::query::schema::{
-        CallInfo, CaseQuery, FailChoice, SampleQualitySettings, SequenceVariant,
+        CallInfo, CaseQuery, FailFilterChoice, SampleQualitySettings, SequenceVariant,
     },
 };
 
@@ -15,7 +15,7 @@ pub struct PassOrNoCall {
 }
 
 /// Determine whether the `SequenceVariant` passes the quality filter.
-/// Will return `FailChoice::Ignore` if the variant passes.
+/// Will return `FailFilterChoice::Ignore` if the variant passes.
 pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result<PassOrNoCall, anyhow::Error> {
     let mut result = PassOrNoCall {
         pass: true,
@@ -25,10 +25,10 @@ pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result<PassOrNoCal
         if let Some(call_info) = seqvar.call_info.get(sample_name) {
             if let Some(fail) = passes_for_sample(quality_settings, call_info) {
                 match fail {
-                    FailChoice::Ignore => {
+                    FailFilterChoice::Ignore => {
                         // ignore quality failure for sample
                     }
-                    FailChoice::Drop => {
+                    FailFilterChoice::Drop => {
                         tracing::trace!(
                             "sample {} (call_info={:?}) in variant {:?} fails quality filter {:?}",
                             &sample_name,
@@ -39,9 +39,6 @@ pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result<PassOrNoCal
                         result.pass = false;
                         break;
                     }
-                    FailChoice::NoCall => {
-                        result.no_call_samples.push(sample_name.clone());
-                    }
                 }
             } else {
                 // no failure, all good
@@ -64,7 +61,7 @@ pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result<PassOrNoCal
 fn passes_for_sample(
     quality_settings: &SampleQualitySettings,
     call_info: &CallInfo,
-) -> Option<FailChoice> {
+) -> Option<FailFilterChoice> {
     #[derive(PartialEq, Eq)]
     enum Genotype {
         Het,
@@ -92,7 +89,7 @@ fn passes_for_sample(
             if let Some(dp_het) = quality_settings.dp_het {
                 if let Some(dp) = call_info.dp {
                     if dp < dp_het {
-                        return Some(FailChoice::Drop); //TODO: Emily Some(quality_settings.fail);
+                        return Some(quality_settings.filter_active);
                     }
                 }
             }
@@ -105,7 +102,7 @@ fn passes_for_sample(
                 let ab = if ab_raw > 0.5 { 1.0 - ab_raw } else { ab_raw };
                 let eps = 1e-6f64;
                 if ab + eps < settings_ab as f64 {
-                    return Some(FailChoice::Drop); // TODO: Emily Some(quality_settings.fail);
+                    return Some(quality_settings.filter_active);
                 }
             }
         }
@@ -113,7 +110,7 @@ fn passes_for_sample(
             if let Some(dp_hom) = quality_settings.dp_hom {
                 if let Some(dp) = call_info.dp {
                     if dp < dp_hom {
-                        return Some(FailChoice::Drop); // TODO: Emily Some(quality_settings.fail);
+                        return Some(quality_settings.filter_active);
                     }
                 }
             }
@@ -124,7 +121,7 @@ fn passes_for_sample(
     // gq
     if let (Some(settings_gq), Some(call_gq)) = (quality_settings.gq, call_info.quality) {
         if call_gq < settings_gq as f32 {
-            return Some(FailChoice::Drop); // TODO: Emily Some(quality_settings.fail);
+            return Some(quality_settings.filter_active);
         }
     }
 
@@ -132,14 +129,14 @@ fn passes_for_sample(
         // ad
         if let (Some(settings_ad), Some(call_ad)) = (quality_settings.ad, call_info.ad) {
             if call_ad < settings_ad {
-                return Some(FailChoice::Drop); // TODO: Emily Some(quality_settings.fail);
+                return Some(quality_settings.filter_active);
             }
         }
 
         // ad_max
         if let (Some(settings_ad_max), Some(call_ad)) = (quality_settings.ad_max, call_info.ad) {
             if call_ad > settings_ad_max {
-                return Some(FailChoice::Drop); // TODO: Emily Some(quality_settings.fail);
+                return Some(quality_settings.filter_active);
             }
         }
     }
@@ -153,7 +150,7 @@ mod test {
 
     use crate::seqvars::query::schema::{
         CallInfo, CaseQuery,
-        FailChoice::{self, *},
+        FailFilterChoice::{self, *},
         SampleQualitySettings, SequenceVariant,
     };
 
@@ -162,10 +159,8 @@ mod test {
     #[case(Ignore, false, true, false)]
     #[case(Drop, true, true, false)]
     #[case(Drop, false, false, false)]
-    #[case(NoCall, true, true, false)]
-    #[case(NoCall, false, true, true)]
     fn passes(
-        #[case] q_fail: FailChoice,
+        #[case] q_fail: FailFilterChoice,
         #[case] should_pass: bool,
         #[case] expected_pass: bool,
         #[case] any_no_call_sample: bool,
@@ -174,13 +169,13 @@ mod test {
             quality: vec![(
                 String::from("sample"),
                 SampleQualitySettings {
+                    filter_active: q_fail,
                     dp_het: None,
                     dp_hom: None,
                     gq: if should_pass { None } else { Some(40) },
                     ab: None,
                     ad: None,
                     ad_max: None,
-                    //TODO: emily fail: q_fail,
                 },
             )]
             .into_iter()
@@ -470,21 +465,21 @@ mod test {
         #[case] q_ab: Option<f32>,
         #[case] q_ad: Option<i32>,
         #[case] q_ad_max: Option<i32>,
-        #[case] q_fail: FailChoice,
+        #[case] q_fail: FailFilterChoice,
         #[case] c_genotype: Option<&'static str>,
         #[case] c_quality: Option<f32>,
         #[case] c_dp: Option<i32>,
         #[case] c_ad: Option<i32>,
-        #[case] expected: Option<FailChoice>,
+        #[case] expected: Option<FailFilterChoice>,
     ) -> Result<(), anyhow::Error> {
         let settings = SampleQualitySettings {
+            filter_active: q_fail,
             dp_het: q_dp_het,
             dp_hom: q_dp_hom,
             gq: q_gq,
             ab: q_ab,
             ad: q_ad,
             ad_max: q_ad_max,
-            //TODO: emily fail: q_fail,
         };
         let call_info = CallInfo {
             genotype: c_genotype.map(|s| s.to_string()),
diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs
index 774286d0..8911fdc7 100644
--- a/src/seqvars/query/mod.rs
+++ b/src/seqvars/query/mod.rs
@@ -488,7 +488,7 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
         rand::rngs::StdRng::from_entropy()
     };
 
-    tracing::info!("Loading query...");
+    tracing::info!("Loading query... {}", args.path_query_json);
     let query: schema::CaseQuery =
         serde_json::from_reader(std::fs::File::open(&args.path_query_json)?)?;
     tracing::info!(
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 5799e2e0..046d5ab5 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -19,33 +19,6 @@ pub enum RecessiveMode {
     CompoundRecessive,
 }
 
-/// Choices for failing quality thresholds on genotypes.
-#[derive(
-    serde::Serialize,
-    serde::Deserialize,
-    PartialEq,
-    Eq,
-    PartialOrd,
-    Ord,
-    Hash,
-    Debug,
-    Clone,
-    Copy,
-    Default,
-    strum::EnumIter,
-)]
-#[serde(rename_all = "kebab-case")]
-pub enum FailChoice {
-    /// Ignore failure.
-    #[default]
-    Ignore,
-    /// Drop whole variant.
-    #[serde(rename = "drop-variant")]
-    Drop,
-    /// Interpret as "no-call".
-    NoCall,
-}
-
 /// Choice for genotype.
 #[derive(
     serde::Serialize,
@@ -114,9 +87,36 @@ impl GenotypeChoice {
     }
 }
 
+/// Choices for failing quality thresholds on genotypes.
+#[derive(
+    serde::Serialize,
+    serde::Deserialize,
+    PartialEq,
+    Eq,
+    PartialOrd,
+    Ord,
+    Hash,
+    Debug,
+    Clone,
+    Copy,
+    Default,
+    strum::EnumIter,
+)]
+#[serde(rename_all = "kebab-case")]
+pub enum FailFilterChoice {
+    /// Ignore failure.
+    #[default]
+    Ignore,
+    /// Drop whole variant.
+    #[serde(rename = "drop-variant")]
+    Drop,
+}
+
 /// Quality settings for one sample.
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
 pub struct SampleQualitySettings {
+    /// Weather to ignore or drop the whole variant on failure
+    pub filter_active: FailFilterChoice,
     /// Minimal coverage for het. sites.
     pub dp_het: Option<i32>,
     /// Minimal coverage for hom. sites.
@@ -134,13 +134,17 @@ pub struct SampleQualitySettings {
 impl From<crate::pbs::seqvars::SampleQualitySettings> for SampleQualitySettings {
     fn from(old: crate::pbs::seqvars::SampleQualitySettings) -> Self {
         Self {
+            filter_active: if old.filter_active {
+                FailFilterChoice::Drop
+            } else {
+                FailFilterChoice::Ignore
+            },
             dp_het: old.dp_het,
             dp_hom: old.dp_hom,
             gq: old.gq,
             ab: old.ab,
             ad: old.ad,
             ad_max: old.ad_max,
-            //fail: FailChoice::iter().nth(old.fail as usize).unwrap(),
         }
     }
 }
@@ -330,7 +334,6 @@ impl From<crate::pbs::seqvars::HelixMtDbOptions> for HelixMtDbOptions {
     }
 }
 
-
 serde_with::with_prefix!(prefix_gnomad_exomes "gnomad_exomes_");
 serde_with::with_prefix!(prefix_gnomad_genomes "gnomad_genomes_");
 serde_with::with_prefix!(prefix_gnomad_mt "gnomat_mt_");
@@ -339,7 +342,6 @@ serde_with::with_prefix!(prefix_gnomad_mt "gnomat_mt_");
 pub struct PopulationFrequencyOptions {
     #[serde(flatten, with = "prefix_gnomad_exomes")]
     pub gnomad_exomes: GnomadNuclearOptions,
-    // TODO emily: flatten right
     #[serde(flatten, with = "prefix_gnomad_genomes")]
     pub gnomad_genomes: GnomadNuclearOptions,
     // gnomAD-MT filter
@@ -479,16 +481,10 @@ pub struct CaseQuery {
 
     /// Genotype choice for each individual.
     pub genotype: indexmap::IndexMap<String, Option<GenotypeChoice>>,
-
-    /// TODO: comment
     #[serde(flatten)]
     pub transcript: TranscriptOptions,
-
-    /// TODO: comment
     #[serde(flatten, with = "prefix_var_type")]
     pub var_type: VariantTypeOptions,
-
-    /// TODO comment
     #[serde(flatten)]
     pub locus: LocusRelatedOptions,
 
@@ -503,7 +499,7 @@ pub struct CaseQuery {
     #[serde(flatten)]
     pub population_frequency: PopulationFrequencyOptions,
 
-    /// Inhouse related filter options. TODO BETTER COMMENT
+    /// Inhouse related filter options.
     #[serde(flatten, with = "prefix_inhouse")]
     pub inhouse: InhouseFrequencyOptions,
 }
@@ -633,7 +629,6 @@ pub struct CallInfo {
     pub phasing_id: Option<i32>,
 }
 
-// serde_with::with_prefix!(prefix_gnomad "gnomad_"); < already declared earlier
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
 pub struct Gnomads {
     /// Number of alleles in gnomAD exomes (not for chrMT).
@@ -667,8 +662,7 @@ pub struct HelixMtDBs {
     pub het: i32,
 }
 
-
-serde_with::with_prefix!(prefix_gnomad "gnomad_"); 
+serde_with::with_prefix!(prefix_gnomad "gnomad_");
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
 
 pub struct PopulationFrequencies {
@@ -678,7 +672,6 @@ pub struct PopulationFrequencies {
     pub helixmtdb: HelixMtDBs,
 }
 
-// serde_with::with_prefix!(prefix_inhouse "inhouse_"); < already declared earlier
 #[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
 pub struct InhouseFrequencies {
     /// Number of in-house alleles (also for chrMT).
@@ -713,7 +706,6 @@ pub struct SequenceVariant {
     /// Mapping of sample to genotype information for the SV.
     pub call_info: indexmap::IndexMap<String, CallInfo>,
 
-    /// TODO: comment
     #[serde(flatten)]
     pub population_frequencies: PopulationFrequencies,
 
@@ -916,8 +908,7 @@ impl SequenceVariant {
         if self.population_frequencies.gnomad.genomes_an == 0 {
             return 0f32;
         }
-        // TODO, emily: is this code hot then check v
-        // This code looks like it could result in some missed oppportunity for optimisation, is it really necessary for hom het and hemi to ever be floats?
+
         let an = self.population_frequencies.gnomad.genomes_an as f32;
         let hom = self.population_frequencies.gnomad.genomes_hom as f32;
         let het = self.population_frequencies.gnomad.genomes_het as f32;
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
index 8bf87bff..30f153aa 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
@@ -70,15 +70,22 @@ clinvar_include_likely_pathogenic: true
 clinvar_include_uncertain_significance: true
 clinvar_include_conflicting_classifications: true
 gnomad_exomes_enabled: false
-gnomad_genomes_enabled: false
-gnomad_exomes_frequency: ~
+gnomad_exomes_carriers: ~
 gnomad_exomes_heterozygous: ~
 gnomad_exomes_homozygous: ~
 gnomad_exomes_hemizygous: ~
-gnomad_genomes_frequency: ~
+gnomad_exomes_frequency: ~
+gnomad_genomes_enabled: false
+gnomad_genomes_carriers: ~
 gnomad_genomes_heterozygous: ~
 gnomad_genomes_homozygous: ~
 gnomad_genomes_hemizygous: ~
+gnomad_genomes_frequency: ~
+gnomat_mt_enabled: false
+gnomat_mt_carriers: ~
+gnomat_mt_heteroplasmic: ~
+gnomat_mt_homoplasmic: ~
+gnomat_mt_frequency: ~
 helixmtdb_enabled: false
 helixmtdb_frequency: ~
 helixmtdb_heteroplasmic: ~
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
index 218169ac..8cfaefe6 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
@@ -54,13 +54,13 @@ consequences:
   - upstream_gene_variant
 quality:
   sample:
+    filter_active: drop-variant
     dp_het: 10
     dp_hom: 5
     gq: 10
     ab: 0.2
     ad: 3
     ad_max: ~
-    fail: drop-variant
 genotype:
   sample: het
 transcripts_coding: true
@@ -79,15 +79,22 @@ clinvar_include_likely_pathogenic: true
 clinvar_include_uncertain_significance: false
 clinvar_include_conflicting_classifications: true
 gnomad_exomes_enabled: true
-gnomad_genomes_enabled: true
-gnomad_exomes_frequency: 0.002
+gnomad_exomes_carriers: ~
 gnomad_exomes_heterozygous: 20
 gnomad_exomes_homozygous: 0
 gnomad_exomes_hemizygous: ~
-gnomad_genomes_frequency: 0.002
+gnomad_exomes_frequency: 0.002
+gnomad_genomes_enabled: true
+gnomad_genomes_carriers: ~
 gnomad_genomes_heterozygous: 4
 gnomad_genomes_homozygous: 0
 gnomad_genomes_hemizygous: ~
+gnomad_genomes_frequency: 0.002
+gnomat_mt_enabled: false
+gnomat_mt_carriers: ~
+gnomat_mt_heteroplasmic: ~
+gnomat_mt_homoplasmic: ~
+gnomat_mt_frequency: ~
 helixmtdb_enabled: true
 helixmtdb_frequency: 0.01
 helixmtdb_heteroplasmic: ~
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
index 218169ac..8cfaefe6 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
@@ -54,13 +54,13 @@ consequences:
   - upstream_gene_variant
 quality:
   sample:
+    filter_active: drop-variant
     dp_het: 10
     dp_hom: 5
     gq: 10
     ab: 0.2
     ad: 3
     ad_max: ~
-    fail: drop-variant
 genotype:
   sample: het
 transcripts_coding: true
@@ -79,15 +79,22 @@ clinvar_include_likely_pathogenic: true
 clinvar_include_uncertain_significance: false
 clinvar_include_conflicting_classifications: true
 gnomad_exomes_enabled: true
-gnomad_genomes_enabled: true
-gnomad_exomes_frequency: 0.002
+gnomad_exomes_carriers: ~
 gnomad_exomes_heterozygous: 20
 gnomad_exomes_homozygous: 0
 gnomad_exomes_hemizygous: ~
-gnomad_genomes_frequency: 0.002
+gnomad_exomes_frequency: 0.002
+gnomad_genomes_enabled: true
+gnomad_genomes_carriers: ~
 gnomad_genomes_heterozygous: 4
 gnomad_genomes_homozygous: 0
 gnomad_genomes_hemizygous: ~
+gnomad_genomes_frequency: 0.002
+gnomat_mt_enabled: false
+gnomat_mt_carriers: ~
+gnomat_mt_heteroplasmic: ~
+gnomat_mt_homoplasmic: ~
+gnomat_mt_frequency: ~
 helixmtdb_enabled: true
 helixmtdb_frequency: 0.01
 helixmtdb_heteroplasmic: ~
diff --git a/tests/seqvars/query/Case_1.query.json b/tests/seqvars/query/Case_1.query.json
index 02d583db..04491f6a 100644
--- a/tests/seqvars/query/Case_1.query.json
+++ b/tests/seqvars/query/Case_1.query.json
@@ -62,7 +62,7 @@
       "ab": 0.2,
       "ad": 3,
       "ad_max": null,
-      "fail": "drop-variant"
+      "filter_active": "drop-variant"
     },
     "Case_1_father-N1-DNA1-WGS1": {
       "dp_het": 10,
@@ -71,7 +71,7 @@
       "ab": 0.2,
       "ad": 3,
       "ad_max": null,
-      "fail": "drop-variant"
+      "filter_active": "drop-variant"
     },
     "Case_1_mother-N1-DNA1-WGS1": {
       "dp_het": 10,
@@ -80,7 +80,7 @@
       "ab": 0.2,
       "ad": 3,
       "ad_max": null,
-      "fail": "drop-variant"
+      "filter_active": "drop-variant"
     }
   },
   "genotype": {
diff --git a/tests/seqvars/query/Case_1.query.json.bak b/tests/seqvars/query/Case_1.query.json.bak
index 61299783..dc2a12a1 100644
--- a/tests/seqvars/query/Case_1.query.json.bak
+++ b/tests/seqvars/query/Case_1.query.json.bak
@@ -62,7 +62,7 @@
       "ab": 0.2,
       "ad": 3,
       "ad_max": null,
-      "fail": "drop-variant"
+      "filter_active": "drop-variant"
     },
     "Case_1_father-N1-DNA1-WGS1": {
       "dp_het": 10,
@@ -71,7 +71,7 @@
       "ab": 0.2,
       "ad": 3,
       "ad_max": null,
-      "fail": "drop-variant"
+      "filter_active": "drop-variant"
     },
     "Case_1_mother-N1-DNA1-WGS1": {
       "dp_het": 10,
@@ -80,7 +80,7 @@
       "ab": 0.2,
       "ad": 3,
       "ad_max": null,
-      "fail": "drop-variant"
+      "filter_active": "drop-variant"
     }
   },
   "genotype": {
diff --git a/tests/seqvars/query/dragen.query.json b/tests/seqvars/query/dragen.query.json
index 568e5e3d..6b1c59cf 100644
--- a/tests/seqvars/query/dragen.query.json
+++ b/tests/seqvars/query/dragen.query.json
@@ -62,7 +62,7 @@
       "ab": 0.2,
       "ad": 3,
       "ad_max": null,
-      "fail": "drop-variant"
+      "filter_active": "drop-variant"
     }
   },
   "genotype": {
diff --git a/tests/seqvars/query/full.json b/tests/seqvars/query/full.json
index 743cd7d9..d6bfe95d 100644
--- a/tests/seqvars/query/full.json
+++ b/tests/seqvars/query/full.json
@@ -46,7 +46,7 @@
       "ab": 0.2,
       "ad": 3,
       "ad_max": null,
-      "fail": "drop-variant"
+      "filter_active": "drop-variant"
     }
   },
   "genotype": {
diff --git a/tests/seqvars/query/with_extra.json b/tests/seqvars/query/with_extra.json
index 1a9d62fb..5e15a17d 100644
--- a/tests/seqvars/query/with_extra.json
+++ b/tests/seqvars/query/with_extra.json
@@ -47,7 +47,7 @@
       "ab": 0.2,
       "ad": 3,
       "ad_max": null,
-      "fail": "drop-variant"
+      "filter_active": "drop-variant"
     }
   },
   "genotype": {

From 70d7c94b106dd7c2d97b1ec1faea33539701775b Mon Sep 17 00:00:00 2001
From: = <=>
Date: Fri, 26 Jul 2024 07:31:32 +0200
Subject: [PATCH 15/23] implement pbjson loading and fix schema

---
 src/seqvars/query/mod.rs                      | 11 +++-
 src/seqvars/query/schema.rs                   | 14 ++--
 ...test__smoke_test_load@with_extra.json.snap | 52 ++++-----------
 tests/seqvars/query/Case_1.query.json         |  2 +-
 tests/seqvars/query/dragen.query.json         |  2 +-
 tests/seqvars/query/full.json                 | 64 ++++++++++++-------
 tests/seqvars/query/with_extra.json           | 20 ++----
 7 files changed, 78 insertions(+), 87 deletions(-)

diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs
index 8911fdc7..417023e4 100644
--- a/src/seqvars/query/mod.rs
+++ b/src/seqvars/query/mod.rs
@@ -489,8 +489,15 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
     };
 
     tracing::info!("Loading query... {}", args.path_query_json);
-    let query: schema::CaseQuery =
-        serde_json::from_reader(std::fs::File::open(&args.path_query_json)?)?;
+    let query: schema::CaseQuery = match serde_json::from_reader(std::fs::File::open(&args.path_query_json)?){ 
+        Ok(query) => query,
+        Err(_) => 
+        {
+            let query: crate::pbs::seqvars::CaseQuery = serde_json::from_reader(std::fs::File::open(&args.path_query_json)?)?;
+            CaseQuery::from(query)
+        },
+    };
+
     tracing::info!(
         "... done loading query = {}",
         &serde_json::to_string(&query)?
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 046d5ab5..0cc67192 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -504,6 +504,7 @@ pub struct CaseQuery {
     pub inhouse: InhouseFrequencyOptions,
 }
 
+// TODO: emily turn into try-from
 impl From<crate::pbs::seqvars::CaseQuery> for CaseQuery {
     fn from(other: crate::pbs::seqvars::CaseQuery) -> Self {
         let consequences: Vec<_> = other
@@ -967,13 +968,16 @@ pub mod test {
     }
 
     #[rstest]
-    #[case("tests/seqvars/query/empty.json")]
-    #[case("tests/seqvars/query/full.json")]
-    #[case("tests/seqvars/query/with_extra.json")]
+    #[case("tests/seqvars/query/empty")]
+    #[case("tests/seqvars/query/full")]
+    #[case("tests/seqvars/query/with_extra")]
     pub fn smoke_test_load(#[case] path_input: &str) -> Result<(), anyhow::Error> {
-        mehari::common::set_snapshot_suffix!("{}", path_input.split('/').last().unwrap());
+        mehari::common::set_snapshot_suffix!("{}.json", path_input.split('/').last().unwrap());
+
+        let query: super::CaseQuery = serde_json::from_reader(std::fs::File::open(format!("{}.json", path_input))?)?;
+        println!("{:#?}", query);
 
-        let query: super::CaseQuery = serde_json::from_reader(std::fs::File::open(path_input)?)?;
+//        let _: crate::pbs::seqvars::CaseQuery = serde_json::from_reader(std::fs::File::open(format!("{}-pb.json", path_input))?)?;
 
         insta::assert_yaml_snapshot!(&query);
 
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
index 8cfaefe6..b7b4762a 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
@@ -3,54 +3,28 @@ source: src/seqvars/query/schema.rs
 expression: "&query"
 ---
 consequences:
-  - chromosome_number_variation
+  - 3_prime_UTR_variant
+  - 5_prime_UTR_variant
+  - disruptive_inframe_deletion
+  - disruptive_inframe_insertion
+  - downstream_gene_variant
   - exon_loss_variant
+  - feature_truncation
   - frameshift_variant
-  - rare_amino_acid_variant
+  - conservative_inframe_deletion
+  - conservative_inframe_insertion
+  - missense_variant
+  - non_coding_transcript_exon_variant
+  - non_coding_transcript_intron_variant
   - splice_acceptor_variant
   - splice_donor_variant
+  - splice_region_variant
   - start_lost
   - stop_gained
   - stop_lost
-  - transcript_ablation
-  - 3_prime_UTR_truncation
-  - 5_prime_UTR_truncation
-  - conservative_inframe_deletion
-  - conservative_inframe_insertion
-  - disruptive_inframe_deletion
-  - disruptive_inframe_insertion
-  - missense_variant
-  - regulatory_region_ablation
-  - splice_region_variant
-  - TFBS_ablation
-  - 5_prime_UTR_premature_start_codon_gain_variant
-  - initiator_codon_variant
-  - start_retained
   - stop_retained_variant
   - synonymous_variant
-  - 3_prime_UTR_variant
-  - 5_prime_UTR_variant
-  - coding_sequence_variant
-  - conserved_intergenic_variant
-  - conserved_intron_variant
-  - downstream_gene_variant
-  - exon_variant
-  - feature_elongation
-  - feature_truncation
-  - gene_variant
-  - intergenic_variant
-  - intron_variant
-  - mature_miRNA_variant
-  - miRNA
-  - NMD_transcript_variant
-  - non_coding_transcript_exon_variant
-  - non_coding_transcript_intron_variant
-  - regulatory_region_amplification
-  - regulatory_region_variant
-  - TF_binding_site_variant
-  - TFBS_amplification
-  - transcript_amplification
-  - transcript_variant
+  - transcript_ablation
   - upstream_gene_variant
 quality:
   sample:
diff --git a/tests/seqvars/query/Case_1.query.json b/tests/seqvars/query/Case_1.query.json
index 04491f6a..e841f1ca 100644
--- a/tests/seqvars/query/Case_1.query.json
+++ b/tests/seqvars/query/Case_1.query.json
@@ -1,5 +1,5 @@
 {
-  "effects": [
+  "consequences": [
     "chromosome_number_variation",
     "exon_loss_variant",
     "frameshift_variant",
diff --git a/tests/seqvars/query/dragen.query.json b/tests/seqvars/query/dragen.query.json
index 6b1c59cf..1e6b33f4 100644
--- a/tests/seqvars/query/dragen.query.json
+++ b/tests/seqvars/query/dragen.query.json
@@ -1,5 +1,5 @@
 {
-  "effects": [
+  "consequences": [
     "chromosome_number_variation",
     "exon_loss_variant",
     "frameshift_variant",
diff --git a/tests/seqvars/query/full.json b/tests/seqvars/query/full.json
index d6bfe95d..b5bc0812 100644
--- a/tests/seqvars/query/full.json
+++ b/tests/seqvars/query/full.json
@@ -1,37 +1,53 @@
 {
-  "effects": [
-    "3_prime_UTR_exon_variant",
-    "3_prime_UTR_intron_variant",
-    "5_prime_UTR_exon_variant",
-    "5_prime_UTR_intron_variant",
-    "coding_transcript_intron_variant",
-    "complex_substitution",
-    "direct_tandem_duplication",
-    "disruptive_inframe_deletion",
-    "disruptive_inframe_insertion",
-    "downstream_gene_variant",
+  "consequences": [
+    "chromosome_number_variation",
     "exon_loss_variant",
-    "feature_truncation",
-    "frameshift_elongation",
-    "frameshift_truncation",
     "frameshift_variant",
-    "inframe_deletion",
-    "inframe_insertion",
-    "internal_feature_elongation",
-    "missense_variant",
-    "mnv",
-    "non_coding_transcript_exon_variant",
-    "non_coding_transcript_intron_variant",
+    "rare_amino_acid_variant",
     "splice_acceptor_variant",
     "splice_donor_variant",
-    "splice_region_variant",
     "start_lost",
     "stop_gained",
     "stop_lost",
+    "transcript_ablation",
+    "3_prime_UTR_truncation",
+    "5_prime_UTR_truncation",
+    "conservative_inframe_deletion",
+    "conservative_inframe_insertion",
+    "disruptive_inframe_deletion",
+    "disruptive_inframe_insertion",
+    "missense_variant",
+    "regulatory_region_ablation",
+    "splice_region_variant",
+    "TFBS_ablation",
+    "5_prime_UTR_premature_start_codon_gain_variant",
+    "initiator_codon_variant",
+    "start_retained",
     "stop_retained_variant",
-    "structural_variant",
     "synonymous_variant",
-    "transcript_ablation",
+    "3_prime_UTR_variant",
+    "5_prime_UTR_variant",
+    "coding_sequence_variant",
+    "conserved_intergenic_variant",
+    "conserved_intron_variant",
+    "downstream_gene_variant",
+    "exon_variant",
+    "feature_elongation",
+    "feature_truncation",
+    "gene_variant",
+    "intergenic_variant",
+    "intron_variant",
+    "mature_miRNA_variant",
+    "miRNA",
+    "NMD_transcript_variant",
+    "non_coding_transcript_exon_variant",
+    "non_coding_transcript_intron_variant",
+    "regulatory_region_amplification",
+    "regulatory_region_variant",
+    "TF_binding_site_variant",
+    "TFBS_amplification",
+    "transcript_amplification",
+    "transcript_variant",
     "upstream_gene_variant"
   ],
   "gnomad_exomes_enabled": true,
diff --git a/tests/seqvars/query/with_extra.json b/tests/seqvars/query/with_extra.json
index 5e15a17d..1a9a5367 100644
--- a/tests/seqvars/query/with_extra.json
+++ b/tests/seqvars/query/with_extra.json
@@ -1,26 +1,17 @@
 {
   "__some_extra__": "42",
-  "effects": [
-    "3_prime_UTR_exon_variant",
-    "3_prime_UTR_intron_variant",
-    "5_prime_UTR_exon_variant",
-    "5_prime_UTR_intron_variant",
-    "coding_transcript_intron_variant",
-    "complex_substitution",
-    "direct_tandem_duplication",
+  "consequences": [
+    "3_prime_UTR_variant",
+    "5_prime_UTR_variant",
     "disruptive_inframe_deletion",
     "disruptive_inframe_insertion",
     "downstream_gene_variant",
     "exon_loss_variant",
     "feature_truncation",
-    "frameshift_elongation",
-    "frameshift_truncation",
     "frameshift_variant",
-    "inframe_deletion",
-    "inframe_insertion",
-    "internal_feature_elongation",
+    "conservative_inframe_deletion",
+    "conservative_inframe_insertion",
     "missense_variant",
-    "mnv",
     "non_coding_transcript_exon_variant",
     "non_coding_transcript_intron_variant",
     "splice_acceptor_variant",
@@ -30,7 +21,6 @@
     "stop_gained",
     "stop_lost",
     "stop_retained_variant",
-    "structural_variant",
     "synonymous_variant",
     "transcript_ablation",
     "upstream_gene_variant"

From 28a99596baaa4884d9dabab1716cbff16ae6a2f1 Mon Sep 17 00:00:00 2001
From: = <=>
Date: Fri, 26 Jul 2024 08:36:21 +0200
Subject: [PATCH 16/23] implement tests for pbjson loading of query

---
 protos/varfish/v1/query_seqvars.proto         |   2 +-
 src/seqvars/query/mod.rs                      |  17 +--
 src/seqvars/query/schema.rs                   |  60 +++++----
 ...hema__test__smoke_test_load@full.json.snap |   2 +-
 tests/seqvars/query/empty-pb.json             |  53 ++++++++
 tests/seqvars/query/full-pb.json              | 126 ++++++++++++++++++
 tests/seqvars/query/full.json                 |   2 +-
 7 files changed, 223 insertions(+), 39 deletions(-)
 create mode 100644 tests/seqvars/query/empty-pb.json
 create mode 100644 tests/seqvars/query/full-pb.json

diff --git a/protos/varfish/v1/query_seqvars.proto b/protos/varfish/v1/query_seqvars.proto
index 3c7cd3a5..c5f4941d 100644
--- a/protos/varfish/v1/query_seqvars.proto
+++ b/protos/varfish/v1/query_seqvars.proto
@@ -220,7 +220,7 @@ message LocusRelatedOptions {
     // List of HGNC symbols, HGNC:<ID>s, ENSG<ID>s, or NCBI Gene IDs to restrict the resulting variants to
     repeated string gene_allowlist = 1;
     // List of genomic regions to limit restrict the resulting variants to
-    repeated GenomicRegion genomic_region = 2;
+    repeated GenomicRegion genomic_regions = 2;
 }
 
 message TranscriptOptions {
diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs
index 417023e4..26442990 100644
--- a/src/seqvars/query/mod.rs
+++ b/src/seqvars/query/mod.rs
@@ -489,14 +489,15 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
     };
 
     tracing::info!("Loading query... {}", args.path_query_json);
-    let query: schema::CaseQuery = match serde_json::from_reader(std::fs::File::open(&args.path_query_json)?){ 
-        Ok(query) => query,
-        Err(_) => 
-        {
-            let query: crate::pbs::seqvars::CaseQuery = serde_json::from_reader(std::fs::File::open(&args.path_query_json)?)?;
-            CaseQuery::from(query)
-        },
-    };
+    let query: schema::CaseQuery =
+        match serde_json::from_reader(std::fs::File::open(&args.path_query_json)?) {
+            Ok(query) => query,
+            Err(_) => {
+                let query: crate::pbs::seqvars::CaseQuery =
+                    serde_json::from_reader(std::fs::File::open(&args.path_query_json)?)?;
+                CaseQuery::from(query)
+            }
+        };
 
     tracing::info!(
         "... done loading query = {}",
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
index 0cc67192..0329b19b 100644
--- a/src/seqvars/query/schema.rs
+++ b/src/seqvars/query/schema.rs
@@ -356,20 +356,20 @@ impl From<crate::pbs::seqvars::PopulationFrequencyOptions> for PopulationFrequen
         Self {
             gnomad_exomes: other
                 .gnomad_exomes
-                .expect("missing field in PopulationFrequencyOptions: gnomad_exomes")
-                .into(),
+                .map(GnomadNuclearOptions::from)
+                .unwrap_or_default(),
             gnomad_genomes: other
                 .gnomad_genomes
-                .expect("missing field in PopulationFrequencyOptions: gnomad_genomes")
-                .into(),
+                .map(GnomadNuclearOptions::from)
+                .unwrap_or_default(),
             gnomad_mt: other
                 .gnomad_mt
-                .expect("missing field in PopulationFrequencyOptions: gnomad_mt")
-                .into(),
+                .map(GnomadMitochondrialOptions::from)
+                .unwrap_or_default(),
             helixmtdb: other
                 .helixmtdb
-                .expect("missing ield in PopulationFrequencyOptions: helixmtdb")
-                .into(),
+                .map(HelixMtDbOptions::from)
+                .unwrap_or_default(),
         }
     }
 }
@@ -423,11 +423,11 @@ impl From<crate::pbs::seqvars::LocusRelatedOptions> for LocusRelatedOptions {
                 None => None,
                 _ => Some(other.gene_allowlist),
             },
-            genomic_regions: match other.genomic_region.first() {
+            genomic_regions: match other.genomic_regions.first() {
                 None => None,
                 _ => Some(
                     other
-                        .genomic_region
+                        .genomic_regions
                         .iter()
                         .map(std::borrow::ToOwned::to_owned)
                         .map(GenomicRegion::from)
@@ -504,7 +504,6 @@ pub struct CaseQuery {
     pub inhouse: InhouseFrequencyOptions,
 }
 
-// TODO: emily turn into try-from
 impl From<crate::pbs::seqvars::CaseQuery> for CaseQuery {
     fn from(other: crate::pbs::seqvars::CaseQuery) -> Self {
         let consequences: Vec<_> = other
@@ -526,29 +525,29 @@ impl From<crate::pbs::seqvars::CaseQuery> for CaseQuery {
                 .iter()
                 .map(|(x, y)| (x.to_owned(), GenotypeChoice::iter().nth(*y as usize)))
                 .collect(),
-            // Protobuf allows retroactively declaring fields optional so we need to enforce presence here
+
             transcript: other
                 .transcript
-                .expect("missing field in CaseQuery: transcript")
-                .into(),
+                .map(TranscriptOptions::from)
+                .unwrap_or_default(),
             var_type: other
                 .var_type
-                .expect("missing field in CaseQuery: var_type")
-                .into(),
+                .map(VariantTypeOptions::from)
+                .unwrap_or_default(),
             locus: other
                 .locus
-                .expect("missing field in CaseQuery: locus")
-                .into(),
-            require_in_clinvar: other.clinvar.is_some(),
-            clinvar: other.clinvar.unwrap_or_default().into(),
+                .map(LocusRelatedOptions::from)
+                .unwrap_or_default(),
+            require_in_clinvar: other.clinvar.clone().unwrap_or_default().require_in_clinvar,
+            clinvar: other.clinvar.map(ClinVarOptions::from).unwrap_or_default(),
             population_frequency: other
                 .population_frequency
-                .expect("Missing field in CaseQuery: population_frequency")
-                .into(),
+                .map(PopulationFrequencyOptions::from)
+                .unwrap_or_default(),
             inhouse: other
                 .inhouse
-                .expect("Missing field in CaseQuery: inhouse")
-                .into(),
+                .map(InhouseFrequencyOptions::from)
+                .unwrap_or_default(),
         }
     }
 }
@@ -974,11 +973,16 @@ pub mod test {
     pub fn smoke_test_load(#[case] path_input: &str) -> Result<(), anyhow::Error> {
         mehari::common::set_snapshot_suffix!("{}.json", path_input.split('/').last().unwrap());
 
-        let query: super::CaseQuery = serde_json::from_reader(std::fs::File::open(format!("{}.json", path_input))?)?;
-        println!("{:#?}", query);
-
-//        let _: crate::pbs::seqvars::CaseQuery = serde_json::from_reader(std::fs::File::open(format!("{}-pb.json", path_input))?)?;
+        let query: super::CaseQuery =
+            serde_json::from_reader(std::fs::File::open(format!("{}.json", path_input))?)?;
 
+        if !path_input.contains("with_extra") {
+            // Check if pbjson loading yields same result
+            let query_pb: crate::pbs::seqvars::CaseQuery =
+                serde_json::from_reader(std::fs::File::open(format!("{}-pb.json", path_input))?)?;
+            let query_pb_conv = super::CaseQuery::from(query_pb);
+            assert_eq!(query, query_pb_conv);
+        }
         insta::assert_yaml_snapshot!(&query);
 
         Ok(())
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
index 8cfaefe6..4129328d 100644
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
+++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
@@ -69,7 +69,7 @@ max_exon_dist: 100
 var_type_snv: true
 var_type_indel: true
 var_type_mnv: true
-gene_allowlist: []
+gene_allowlist: ~
 genomic_regions: ~
 require_in_clinvar: false
 clinvar_include_benign: false
diff --git a/tests/seqvars/query/empty-pb.json b/tests/seqvars/query/empty-pb.json
new file mode 100644
index 00000000..1a8da685
--- /dev/null
+++ b/tests/seqvars/query/empty-pb.json
@@ -0,0 +1,53 @@
+{
+    "consequences": [
+    "ChromosomeNumberVariation",
+    "ExonLossVariant",
+    "FrameshiftVariant",
+    "RareAminoAcidVariant",
+    "SpliceAcceptorVariant",
+    "SpliceDonorVariant",
+    "StartLost",
+    "StopGained",
+    "StopLost",
+    "TranscriptAblation",
+    "ThreePrimeUtrTruncation",
+    "FivePrimeUtrTruncaction",
+    "ConservativeInframeDeletion",
+    "ConservativeInframeInsertion",
+    "DisruptiveInframeDeletion",
+    "DisruptiveInframeInsertion",
+    "MissenseVariant",
+    "RegulatoryRegionAblation",
+    "SpliceRegionVariant",
+    "TbfsAblation",
+    "FivePrimeUtrPrematureStartCodonGainVariant",
+    "InitiatorCodonVariant",
+    "StartRetained",
+    "StopRetainedVariant",
+    "SynonymousVariant",
+    "ThreePrimeUtrVariant",
+    "FivePrimeUtrVariant",
+    "CodingSequenceVariant",
+    "ConservedIntergenicVariant",
+    "ConservedIntronVariant",
+    "DownstreamGeneVariant",
+    "ExonVariant",
+    "FeatureElongation",
+    "FeatureTruncation",
+    "GeneVariant",
+    "IntergenicVariant",
+    "IntronVariant",
+    "MatureMirnaVariant",
+    "Mirna",
+    "NmdTranscriptVariant",
+    "NonCodingTranscriptExonVariant",
+    "NonCodingTranscriptIntronVariant",
+    "RegulatoryRegionAmplification",
+    "RegulatoryRegionVariant",
+    "TfBindingSiteVariant",
+    "TfbsAmplification",
+    "TranscriptAmplification",
+    "TranscriptVariant",
+    "UpstreamGeneVariant"
+  ]
+}
diff --git a/tests/seqvars/query/full-pb.json b/tests/seqvars/query/full-pb.json
new file mode 100644
index 00000000..21e8faa9
--- /dev/null
+++ b/tests/seqvars/query/full-pb.json
@@ -0,0 +1,126 @@
+{
+  "consequences": [
+    "ChromosomeNumberVariation",
+    "ExonLossVariant",
+    "FrameshiftVariant",
+    "RareAminoAcidVariant",
+    "SpliceAcceptorVariant",
+    "SpliceDonorVariant",
+    "StartLost",
+    "StopGained",
+    "StopLost",
+    "TranscriptAblation",
+    "ThreePrimeUtrTruncation",
+    "FivePrimeUtrTruncaction",
+    "ConservativeInframeDeletion",
+    "ConservativeInframeInsertion",
+    "DisruptiveInframeDeletion",
+    "DisruptiveInframeInsertion",
+    "MissenseVariant",
+    "RegulatoryRegionAblation",
+    "SpliceRegionVariant",
+    "TbfsAblation",
+    "FivePrimeUtrPrematureStartCodonGainVariant",
+    "InitiatorCodonVariant",
+    "StartRetained",
+    "StopRetainedVariant",
+    "SynonymousVariant",
+    "ThreePrimeUtrVariant",
+    "FivePrimeUtrVariant",
+    "CodingSequenceVariant",
+    "ConservedIntergenicVariant",
+    "ConservedIntronVariant",
+    "DownstreamGeneVariant",
+    "ExonVariant",
+    "FeatureElongation",
+    "FeatureTruncation",
+    "GeneVariant",
+    "IntergenicVariant",
+    "IntronVariant",
+    "MatureMirnaVariant",
+    "Mirna",
+    "NmdTranscriptVariant",
+    "NonCodingTranscriptExonVariant",
+    "NonCodingTranscriptIntronVariant",
+    "RegulatoryRegionAmplification",
+    "RegulatoryRegionVariant",
+    "TfBindingSiteVariant",
+    "TfbsAmplification",
+    "TranscriptAmplification",
+    "TranscriptVariant",
+    "UpstreamGeneVariant"
+  ],
+  "population_frequency": {
+    "gnomad_exomes": {
+      "enabled": true,
+      "allele_frequency": 0.002,
+      "heterozygous": 20,
+      "homozygous": 0,
+      "hemizygous": null
+    },
+    "gnomad_genomes": {
+      "enabled": true,
+      "allele_frequency": 0.002,
+      "heterozygous": 4,
+      "homozygous": 0,
+      "hemizygous": null
+    },
+    "gnomad_mt": {
+      "enabled": false,
+      "allele_frequency": null,
+      "heteroplasmic": null,
+      "homoplasmic": null,
+      "carriers": null
+    },
+    "helixmtdb": {
+      "enabled": true,
+      "frequency": 0.01,
+      "heteroplasmic": null,
+      "homoplasmic": null
+    }
+  },
+  "inhouse": {
+    "enabled": true,
+    "carriers": 20,
+    "heterozygous": null,
+    "homozygous": null,
+    "hemizygous": null
+  },
+  "quality": {
+    "sample": {
+      "dp_het": 10,
+      "dp_hom": 5,
+      "gq": 10,
+      "ab": 0.2,
+      "ad": 3,
+      "ad_max": null,
+      "filter_active": true
+    }
+  },
+  "genotype": {
+    "sample": "Het"
+  },
+  "clinvar": {
+    "require_in_clinvar": false,
+    "include_benign": false,
+    "include_pathogenic": true,
+    "include_likely_benign": false,
+    "include_likely_pathogenic": true,
+    "include_uncertain_significance": false,
+    "include_conflicting_classifications": true
+  },
+  "transcript": {
+    "transcripts_coding": true,
+    "transcripts_noncoding": true,
+    "max_exon_dist": 100
+  },
+  "var_type": {
+    "snv": true,
+    "indel": true,
+    "mnv": true
+  },
+  "locus": {
+    "gene_allowlist": [],
+    "genomic_regions": []  
+  }
+}
diff --git a/tests/seqvars/query/full.json b/tests/seqvars/query/full.json
index b5bc0812..8c85c4e0 100644
--- a/tests/seqvars/query/full.json
+++ b/tests/seqvars/query/full.json
@@ -75,7 +75,7 @@
   "var_type_indel": true,
   "var_type_mnv": true,
   "max_exon_dist": 100,
-  "gene_allowlist": [],
+  "gene_allowlist": null,
   "genomic_regions": null,
   "require_in_clinvar": false,
   "clinvar_include_benign": false,

From 92ffa3b9f59063cd5e8909a2a42161ef1a6edc25 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Fri, 2 Aug 2024 15:13:27 +0200
Subject: [PATCH 17/23] wip

---
 Cargo.lock                                    |  485 +++-
 Cargo.toml                                    |   10 +-
 build.rs                                      |    2 +-
 protos/varfish/v1/query_seqvars.proto         |  251 --
 protos/varfish/v1/seqvars/query.proto         |  341 +++
 protos/varfish/v1/worker.proto                |   32 +-
 src/common/mod.rs                             |   14 +-
 src/pbs.rs                                    |   23 +-
 src/seqvars/ingest/header.rs                  |   32 +
 src/seqvars/ingest/mod.rs                     |    6 +-
 src/seqvars/query/annonars.rs                 |   48 +-
 src/seqvars/query/interpreter/clinvar.rs      |   36 +-
 src/seqvars/query/interpreter/consequences.rs |   52 +-
 src/seqvars/query/interpreter/frequency.rs    |  290 ++-
 .../query/interpreter/genes_allowlist.rs      |   66 +-
 src/seqvars/query/interpreter/genotype.rs     |  423 ++--
 src/seqvars/query/interpreter/mod.rs          |   12 +-
 src/seqvars/query/interpreter/quality.rs      |  441 ++--
 .../query/interpreter/regions_allowlist.rs    |   47 +-
 src/seqvars/query/mod.rs                      |  237 +-
 src/seqvars/query/output/call_related.rs      |   10 +-
 src/seqvars/query/output/gene_related.rs      |    8 +-
 src/seqvars/query/output/variant_related.rs   |   50 +-
 src/seqvars/query/schema.rs                   | 1016 --------
 src/seqvars/query/schema/data.rs              |  714 ++++++
 src/seqvars/query/schema/mod.rs               |    4 +
 src/seqvars/query/schema/query.rs             | 2197 +++++++++++++++++
 ...riant_from_vcf@Case_1.ingested.vcf-10.snap |  156 --
 ...riant_from_vcf@Case_1.ingested.vcf-11.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-12.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-13.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-14.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-15.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-16.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-17.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-18.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-19.snap |   43 -
 ...ariant_from_vcf@Case_1.ingested.vcf-2.snap |  155 --
 ...riant_from_vcf@Case_1.ingested.vcf-20.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-21.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-22.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-23.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-24.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-25.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-26.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-27.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-28.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-29.snap |   43 -
 ...ariant_from_vcf@Case_1.ingested.vcf-3.snap |  155 --
 ...riant_from_vcf@Case_1.ingested.vcf-30.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-31.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-32.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-33.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-34.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-35.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-36.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-37.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-38.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-39.snap |   43 -
 ...ariant_from_vcf@Case_1.ingested.vcf-4.snap |  155 --
 ...riant_from_vcf@Case_1.ingested.vcf-40.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-41.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-42.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-43.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-44.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-45.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-46.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-47.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-48.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-49.snap |   43 -
 ...ariant_from_vcf@Case_1.ingested.vcf-5.snap |  156 --
 ...riant_from_vcf@Case_1.ingested.vcf-50.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-51.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-52.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-53.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-54.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-55.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-56.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-57.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-58.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-59.snap |   43 -
 ...ariant_from_vcf@Case_1.ingested.vcf-6.snap |  155 --
 ...riant_from_vcf@Case_1.ingested.vcf-60.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-61.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-62.snap |   43 -
 ...riant_from_vcf@Case_1.ingested.vcf-63.snap |   43 -
 ...ariant_from_vcf@Case_1.ingested.vcf-7.snap |  155 --
 ...ariant_from_vcf@Case_1.ingested.vcf-8.snap |  155 --
 ...ariant_from_vcf@Case_1.ingested.vcf-9.snap |  155 --
 ..._variant_from_vcf@Case_1.ingested.vcf.snap |  167 --
 ...ariant_from_vcf@dragen.ingested.vcf-2.snap |   31 -
 ..._variant_from_vcf@dragen.ingested.vcf.snap |  143 --
 ...ema__test__smoke_test_load@empty.json.snap |   97 -
 ...hema__test__smoke_test_load@full.json.snap |  106 -
 ...test__smoke_test_load@with_extra.json.snap |   80 -
 ..._test__smoke_test@Case_1.ingested.vcf.snap |   64 -
 ..._test__smoke_test@dragen.ingested.vcf.snap |    7 -
 src/seqvars/query/sorting.rs                  |   22 +-
 src/strucvars/query/mod.rs                    |   11 +-
 99 files changed, 4603 insertions(+), 6648 deletions(-)
 delete mode 100644 protos/varfish/v1/query_seqvars.proto
 create mode 100644 protos/varfish/v1/seqvars/query.proto
 delete mode 100644 src/seqvars/query/schema.rs
 create mode 100644 src/seqvars/query/schema/data.rs
 create mode 100644 src/seqvars/query/schema/mod.rs
 create mode 100644 src/seqvars/query/schema/query.rs
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap
 delete mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap
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diff --git a/Cargo.lock b/Cargo.lock
index 7c847829..ea229200 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -133,9 +133,9 @@ dependencies = [
 
 [[package]]
 name = "actix-web"
-version = "4.7.0"
+version = "4.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5d6316df3fa569627c98b12557a8b6ff0674e5be4bb9b5e4ae2550ddb4964ed6"
+checksum = "1988c02af8d2b718c05bc4aeb6a66395b7cdf32858c2c71131e5637a8c05a9ff"
 dependencies = [
  "actix-codec",
  "actix-http",
@@ -270,14 +270,14 @@ dependencies = [
 
 [[package]]
 name = "annonars"
-version = "0.39.0"
+version = "0.40.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "37532e1e083ca6dcc0a1420ad7d8b718c78103d325222749d8d7091237d19aaf"
+checksum = "8f1a0363fc4a6c133dedd77510768c1292da2aa915054db1e5e4436732997efe"
 dependencies = [
  "actix-web",
  "anyhow",
  "bgzip",
- "bio",
+ "bio 2.0.1",
  "biocommons-bioutils",
  "boolvec",
  "byteorder",
@@ -293,16 +293,16 @@ dependencies = [
  "indicatif",
  "itertools 0.13.0",
  "log",
- "noodles",
- "pbjson",
- "pbjson-build",
- "pbjson-types",
- "prost",
- "prost-build",
+ "noodles 0.77.0",
+ "pbjson 0.7.0",
+ "pbjson-build 0.7.0",
+ "pbjson-types 0.7.0",
+ "prost 0.13.1",
+ "prost-build 0.13.1",
  "rayon",
  "rocksdb",
  "rocksdb-utils-lookup",
- "rustc-hash",
+ "rustc-hash 2.0.0",
  "serde",
  "serde_json",
  "serde_with",
@@ -1027,7 +1027,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "regex",
- "rustc-hash",
+ "rustc-hash 1.1.0",
  "shlex",
  "syn 2.0.66",
 ]
@@ -1041,7 +1041,7 @@ dependencies = [
  "anyhow",
  "approx",
  "bio-types",
- "bit-set",
+ "bit-set 0.5.3",
  "bv",
  "bytecount",
  "csv",
@@ -1057,7 +1057,7 @@ dependencies = [
  "newtype_derive",
  "num-integer",
  "num-traits",
- "ordered-float",
+ "ordered-float 3.9.2",
  "petgraph",
  "rand",
  "regex",
@@ -1071,6 +1071,45 @@ dependencies = [
  "vec_map",
 ]
 
+[[package]]
+name = "bio"
+version = "2.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e8cbd545253762ecf9ef741f2c49f07c06a0ce4d041d74ee9c3f1ce0e2d5446e"
+dependencies = [
+ "anyhow",
+ "approx",
+ "bio-types",
+ "bit-set 0.8.0",
+ "bv",
+ "bytecount",
+ "csv",
+ "custom_derive",
+ "editdistancek",
+ "enum-map",
+ "fxhash",
+ "itertools 0.13.0",
+ "itertools-num",
+ "lazy_static",
+ "multimap 0.10.0",
+ "ndarray",
+ "newtype_derive",
+ "num-integer",
+ "num-traits",
+ "ordered-float 4.2.2",
+ "petgraph",
+ "rand",
+ "regex",
+ "serde",
+ "serde_derive",
+ "statrs",
+ "strum 0.26.3",
+ "strum_macros 0.26.4",
+ "thiserror",
+ "triple_accel",
+ "vec_map",
+]
+
 [[package]]
 name = "bio-types"
 version = "1.0.1"
@@ -1104,7 +1143,16 @@ version = "0.5.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1"
 dependencies = [
- "bit-vec",
+ "bit-vec 0.6.3",
+]
+
+[[package]]
+name = "bit-set"
+version = "0.8.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "08807e080ed7f9d5433fa9b275196cfc35414f66a0c79d864dc51a0d825231a3"
+dependencies = [
+ "bit-vec 0.8.0",
 ]
 
 [[package]]
@@ -1113,6 +1161,12 @@ version = "0.6.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb"
 
+[[package]]
+name = "bit-vec"
+version = "0.8.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5e764a1d40d510daf35e07be9eb06e75770908c27d411ee6c92109c9840eaaf7"
+
 [[package]]
 name = "bitflags"
 version = "1.3.2"
@@ -1341,24 +1395,24 @@ dependencies = [
 
 [[package]]
 name = "cached"
-version = "0.50.0"
+version = "0.53.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "10a7d38ed2761b8a13ce42bc44b09d5a052b88da2f9fead624c779f31ac0729a"
+checksum = "b4d73155ae6b28cf5de4cfc29aeb02b8a1c6dab883cb015d15cd514e42766846"
 dependencies = [
  "ahash 0.8.11",
  "cached_proc_macro",
  "cached_proc_macro_types",
  "hashbrown 0.14.5",
- "instant",
  "once_cell",
  "thiserror",
+ "web-time",
 ]
 
 [[package]]
 name = "cached_proc_macro"
-version = "0.21.0"
+version = "0.23.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "771aa57f3b17da6c8bcacb187bb9ec9bc81c8160e72342e67c329e0e1651a669"
+checksum = "2f42a145ed2d10dce2191e1dcf30cfccfea9026660e143662ba5eec4017d5daa"
 dependencies = [
  "darling",
  "proc-macro2",
@@ -1520,6 +1574,15 @@ version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6245d59a3e82a7fc217c5828a6692dbc6dfb63a0c8c90495621f7b9d79704a0e"
 
+[[package]]
+name = "convert_case"
+version = "0.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ec182b0ca2f35d8fc196cf3404988fd8b8c739a4d270ff118a398feb0cbec1ca"
+dependencies = [
+ "unicode-segmentation",
+]
+
 [[package]]
 name = "cookie"
 version = "0.16.2"
@@ -1822,7 +1885,7 @@ version = "0.99.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5f33878137e4dafd7fa914ad4e259e18a4e8e532b9617a2d0150262bf53abfce"
 dependencies = [
- "convert_case",
+ "convert_case 0.4.0",
  "proc-macro2",
  "quote",
  "rustc_version 0.4.0",
@@ -1839,7 +1902,7 @@ dependencies = [
  "lazy_static",
  "mintex",
  "parking_lot",
- "rustc-hash",
+ "rustc-hash 1.1.0",
  "serde",
  "serde_json",
  "thousands",
@@ -1963,6 +2026,27 @@ dependencies = [
  "syn 2.0.66",
 ]
 
+[[package]]
+name = "enumflags2"
+version = "0.7.10"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d232db7f5956f3f14313dc2f87985c58bd2c695ce124c8cdd984e08e15ac133d"
+dependencies = [
+ "enumflags2_derive",
+ "serde",
+]
+
+[[package]]
+name = "enumflags2_derive"
+version = "0.7.10"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "de0d48a183585823424a4ce1aa132d174a6a81bd540895822eb4c8373a8e49e8"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.66",
+]
+
 [[package]]
 name = "env_filter"
 version = "0.1.0"
@@ -2422,13 +2506,13 @@ checksum = "7f24254aa9a54b5c858eaee2f5bccdb46aaf0e486a595ed5fd8f86ba55232a70"
 
 [[package]]
 name = "hgvs"
-version = "0.16.1"
+version = "0.17.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c860777179557614169d38d0ef292aff2e14aa2a95464dba6654c6753b4d0998"
+checksum = "bc11f5c31ad6f61ff160ed587ed67a6cdc677acc22e316ab6451c01e1bf17fb3"
 dependencies = [
  "ahash 0.8.11",
  "base16ct 0.2.0",
- "bio",
+ "bio 2.0.1",
  "biocommons-bioutils",
  "cached",
  "chrono",
@@ -2442,7 +2526,7 @@ dependencies = [
  "postgres",
  "quick_cache",
  "regex",
- "rustc-hash",
+ "rustc-hash 2.0.0",
  "seqrepo",
  "serde",
  "serde_json",
@@ -2754,6 +2838,27 @@ dependencies = [
  "thiserror",
 ]
 
+[[package]]
+name = "kinded"
+version = "0.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ce4bdbb2f423660b19f0e9f7115182214732d8dd5f840cd0a3aee3e22562f34c"
+dependencies = [
+ "kinded_macros",
+]
+
+[[package]]
+name = "kinded_macros"
+version = "0.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a13b4ddc5dcb32f45dac3d6f606da2a52fdb9964a18427e63cd5ef6c0d13288d"
+dependencies = [
+ "convert_case 0.6.0",
+ "proc-macro2",
+ "quote",
+ "syn 2.0.66",
+]
+
 [[package]]
 name = "kv-log-macro"
 version = "1.0.7"
@@ -3029,16 +3134,16 @@ dependencies = [
 
 [[package]]
 name = "mehari"
-version = "0.25.7"
+version = "0.26.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5eb3776b15b1b0d1199cd1c60fdeb806aee0fd9a56d064992ee566d1f9fe43c7"
+checksum = "462ca9aa32beb2b638552cb931c5cbb40c01a025e6235ebab2e633bcef612af5"
 dependencies = [
  "actix-web",
  "annonars",
  "anyhow",
  "async-compression",
  "bgzip",
- "bio",
+ "bio 2.0.1",
  "biocommons-bioutils",
  "byte-unit",
  "byteorder",
@@ -3048,8 +3153,10 @@ dependencies = [
  "coz",
  "csv",
  "derivative",
+ "derive-new 0.6.0",
  "derive_builder",
  "dhat",
+ "enumflags2",
  "env_logger",
  "flate2",
  "futures",
@@ -3058,22 +3165,24 @@ dependencies = [
  "indicatif",
  "itertools 0.13.0",
  "jsonl",
- "lazy_static",
  "log",
  "nom",
- "noodles",
+ "noodles 0.77.0",
+ "nutype",
+ "once_cell",
  "parse-display",
- "pbjson",
- "pbjson-build",
- "pbjson-types",
+ "pbjson 0.7.0",
+ "pbjson-build 0.7.0",
+ "pbjson-types 0.7.0",
  "procfs",
- "prost",
- "prost-build",
+ "prost 0.13.1",
+ "prost-build 0.13.1",
  "quick_cache",
  "rand",
  "rand_core",
+ "rayon",
  "rocksdb",
- "rustc-hash",
+ "rustc-hash 2.0.0",
  "seqrepo",
  "serde",
  "serde_json",
@@ -3218,15 +3327,26 @@ name = "noodles"
 version = "0.76.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7a346e5a6000033512105890243ff310a307637ae9d9de317f7480e136549a4d"
+dependencies = [
+ "noodles-bgzf 0.30.0",
+ "noodles-core",
+ "noodles-fasta 0.39.0",
+]
+
+[[package]]
+name = "noodles"
+version = "0.77.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6f8629ce12eeb2d6483be18af64beb9488840299ecd617be4ec2f4ebf66688e6"
 dependencies = [
  "noodles-bam",
  "noodles-bcf",
  "noodles-bed",
- "noodles-bgzf",
+ "noodles-bgzf 0.31.0",
  "noodles-core",
  "noodles-cram",
  "noodles-csi",
- "noodles-fasta",
+ "noodles-fasta 0.40.0",
  "noodles-fastq",
  "noodles-gff",
  "noodles-sam",
@@ -3236,17 +3356,17 @@ dependencies = [
 
 [[package]]
 name = "noodles-bam"
-version = "0.63.0"
+version = "0.64.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3ede0b1e0b8e0e03f21c692ad38473dfe95c3650317650205c29c9a682c4a5a6"
+checksum = "3fd4e9825cce4ed3c7fa958efce37268d899bdb7fdeb22d73493a095de1564be"
 dependencies = [
- "bit-vec",
+ "bit-vec 0.6.3",
  "bstr",
  "byteorder",
  "bytes",
  "futures",
  "indexmap 2.2.6",
- "noodles-bgzf",
+ "noodles-bgzf 0.31.0",
  "noodles-core",
  "noodles-csi",
  "noodles-sam",
@@ -3255,14 +3375,14 @@ dependencies = [
 
 [[package]]
 name = "noodles-bcf"
-version = "0.56.0"
+version = "0.57.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "84399185965e44a6fe2ea499cf2bc81e4e687bde7b39de5e8fa5b72c6a0a0982"
+checksum = "303f875dac987f76fcf05e133811e3ccc25c8649151569e7c8003f25d78b7aa8"
 dependencies = [
  "byteorder",
  "futures",
  "indexmap 2.2.6",
- "noodles-bgzf",
+ "noodles-bgzf 0.31.0",
  "noodles-core",
  "noodles-csi",
  "noodles-vcf",
@@ -3271,9 +3391,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-bed"
-version = "0.14.0"
+version = "0.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1d114cc62a405cc763e0e0607a037e5bb9298e281690f9e10bc2ffc2312f92b3"
+checksum = "4c781b824d10b621df17d26fb5cd9d3cc8188aeabda7de7e36cde51f6015b31d"
 dependencies = [
  "noodles-core",
 ]
@@ -3283,6 +3403,18 @@ name = "noodles-bgzf"
 version = "0.30.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "13f54d4840fd26ed94103ded9524aa5fdd757255a556f24653d162c0a45c47e8"
+dependencies = [
+ "byteorder",
+ "bytes",
+ "crossbeam-channel",
+ "flate2",
+]
+
+[[package]]
+name = "noodles-bgzf"
+version = "0.31.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "754f4d28655c5d486e2a62814c5dcc46ad2cee5a2b6cbe91fd765a5ec997f91a"
 dependencies = [
  "byteorder",
  "bytes",
@@ -3305,9 +3437,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-cram"
-version = "0.64.0"
+version = "0.65.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0139e7b11f63244be14ce5abe53e9379ba25d7a606424dcb0f40b5c31831f6e7"
+checksum = "4cf95f7e286f62550121f6135a1cb372a0233eba7bffb7f7bebe55eb4f12b35c"
 dependencies = [
  "async-compression",
  "bitflags 2.5.0",
@@ -3321,7 +3453,7 @@ dependencies = [
  "md-5",
  "noodles-bam",
  "noodles-core",
- "noodles-fasta",
+ "noodles-fasta 0.40.0",
  "noodles-sam",
  "pin-project-lite",
  "tokio",
@@ -3330,14 +3462,14 @@ dependencies = [
 
 [[package]]
 name = "noodles-csi"
-version = "0.35.0"
+version = "0.36.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "beb1618ca2aa88662d387197a188686105d6b5e25f6959c52b766276cbfc4620"
+checksum = "89ac24bac459ae99c046086d771f5a79f632ab27a9280406f2fbb7a3238d79cc"
 dependencies = [
- "bit-vec",
+ "bit-vec 0.6.3",
  "byteorder",
  "indexmap 2.2.6",
- "noodles-bgzf",
+ "noodles-bgzf 0.31.0",
  "noodles-core",
  "tokio",
 ]
@@ -3350,16 +3482,29 @@ checksum = "c3f35c5b39977f95efacb67c3ae4ca00b5229249327bb0e9a980f386cad36d93"
 dependencies = [
  "bytes",
  "memchr",
- "noodles-bgzf",
+ "noodles-bgzf 0.30.0",
+ "noodles-core",
+]
+
+[[package]]
+name = "noodles-fasta"
+version = "0.40.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "195e5a37b273b03499d85a83e9101532c02a21c7b9b2d9c11960b6fbfdcd39ad"
+dependencies = [
+ "bstr",
+ "bytes",
+ "memchr",
+ "noodles-bgzf 0.31.0",
  "noodles-core",
  "tokio",
 ]
 
 [[package]]
 name = "noodles-fastq"
-version = "0.11.0"
+version = "0.12.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fc408c8c4ce6806d2ebadef2fa2fe20f32ec98769f035d637564d6f2d08b7769"
+checksum = "07822ab5042903a710fedc1ac86e08c18dfc1bd87af404e938efa3df212c1011"
 dependencies = [
  "futures",
  "memchr",
@@ -3368,13 +3513,13 @@ dependencies = [
 
 [[package]]
 name = "noodles-gff"
-version = "0.33.0"
+version = "0.34.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "578b6efaf5c3f029720af4c8590e34fd38e214666971d665a52e3566830170d0"
+checksum = "1461ade66be950a9c4ad10839f960a50b41c4174471ff904350d203e57a052b1"
 dependencies = [
  "futures",
  "indexmap 2.2.6",
- "noodles-bgzf",
+ "noodles-bgzf 0.31.0",
  "noodles-core",
  "noodles-csi",
  "percent-encoding",
@@ -3383,9 +3528,9 @@ dependencies = [
 
 [[package]]
 name = "noodles-sam"
-version = "0.60.0"
+version = "0.61.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0ec6452e8ed9f20ef043dce35e09ed58f1c34834cd941e987458a66e8fa66fa0"
+checksum = "48e2636562b1b13e21369e82b0426cd532a3fb2dc676eccec89215a1a8dad243"
 dependencies = [
  "bitflags 2.5.0",
  "bstr",
@@ -3393,7 +3538,7 @@ dependencies = [
  "indexmap 2.2.6",
  "lexical-core",
  "memchr",
- "noodles-bgzf",
+ "noodles-bgzf 0.31.0",
  "noodles-core",
  "noodles-csi",
  "tokio",
@@ -3401,14 +3546,14 @@ dependencies = [
 
 [[package]]
 name = "noodles-tabix"
-version = "0.41.0"
+version = "0.42.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0cc110f78cb406f69f42c482d1986526c590b7295f37f0e37f1fc380413400ef"
+checksum = "8ddf20eb2a380e00bbe6ec3105f1ef5c62307381f4bcf4175b31d582d43a7e59"
 dependencies = [
- "bit-vec",
+ "bit-vec 0.6.3",
  "byteorder",
  "indexmap 2.2.6",
- "noodles-bgzf",
+ "noodles-bgzf 0.31.0",
  "noodles-core",
  "noodles-csi",
  "tokio",
@@ -3416,14 +3561,14 @@ dependencies = [
 
 [[package]]
 name = "noodles-vcf"
-version = "0.59.0"
+version = "0.60.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7363b498e8a015db55777ccbc5cb0036182175851443c62ef847c7152c8a9919"
+checksum = "adb37ce398cc0132b5855ac720c2e9efe14270b38be57ee576d79bc918754e2a"
 dependencies = [
  "futures",
  "indexmap 2.2.6",
  "memchr",
- "noodles-bgzf",
+ "noodles-bgzf 0.31.0",
  "noodles-core",
  "noodles-csi",
  "noodles-tabix",
@@ -3502,6 +3647,29 @@ version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3"
 
+[[package]]
+name = "nutype"
+version = "0.4.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "362399c4581483ed2813c9b05dd6bcd903c60e61005c4b838c65ae755be69dd6"
+dependencies = [
+ "nutype_macros",
+]
+
+[[package]]
+name = "nutype_macros"
+version = "0.4.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0625bcc0c714bdf12a451c4f6510b949abb095d98cc3cc8fe3812a8100ca6592"
+dependencies = [
+ "cfg-if",
+ "kinded",
+ "proc-macro2",
+ "quote",
+ "syn 2.0.66",
+ "urlencoding",
+]
+
 [[package]]
 name = "object"
 version = "0.36.0"
@@ -3538,6 +3706,15 @@ dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "ordered-float"
+version = "4.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4a91171844676f8c7990ce64959210cd2eaef32c2612c50f9fae9f8aaa6065a6"
+dependencies = [
+ "num-traits",
+]
+
 [[package]]
 name = "outref"
 version = "0.5.1"
@@ -3631,6 +3808,16 @@ dependencies = [
  "serde",
 ]
 
+[[package]]
+name = "pbjson"
+version = "0.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c7e6349fa080353f4a597daffd05cb81572a9c031a6d4fff7e504947496fcc68"
+dependencies = [
+ "base64 0.21.7",
+ "serde",
+]
+
 [[package]]
 name = "pbjson-build"
 version = "0.6.2"
@@ -3639,8 +3826,20 @@ checksum = "2580e33f2292d34be285c5bc3dba5259542b083cfad6037b6d70345f24dcb735"
 dependencies = [
  "heck 0.4.1",
  "itertools 0.11.0",
- "prost",
- "prost-types",
+ "prost 0.12.6",
+ "prost-types 0.12.6",
+]
+
+[[package]]
+name = "pbjson-build"
+version = "0.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6eea3058763d6e656105d1403cb04e0a41b7bbac6362d413e7c33be0c32279c9"
+dependencies = [
+ "heck 0.5.0",
+ "itertools 0.13.0",
+ "prost 0.13.1",
+ "prost-types 0.13.1",
 ]
 
 [[package]]
@@ -3651,10 +3850,25 @@ checksum = "18f596653ba4ac51bdecbb4ef6773bc7f56042dc13927910de1684ad3d32aa12"
 dependencies = [
  "bytes",
  "chrono",
- "pbjson",
- "pbjson-build",
- "prost",
- "prost-build",
+ "pbjson 0.6.0",
+ "pbjson-build 0.6.2",
+ "prost 0.12.6",
+ "prost-build 0.12.6",
+ "serde",
+]
+
+[[package]]
+name = "pbjson-types"
+version = "0.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e54e5e7bfb1652f95bc361d76f3c780d8e526b134b85417e774166ee941f0887"
+dependencies = [
+ "bytes",
+ "chrono",
+ "pbjson 0.7.0",
+ "pbjson-build 0.7.0",
+ "prost 0.13.1",
+ "prost-build 0.13.1",
  "serde",
 ]
 
@@ -3918,7 +4132,17 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "deb1435c188b76130da55f17a466d252ff7b1418b2ad3e037d127b94e3411f29"
 dependencies = [
  "bytes",
- "prost-derive",
+ "prost-derive 0.12.6",
+]
+
+[[package]]
+name = "prost"
+version = "0.13.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e13db3d3fde688c61e2446b4d843bc27a7e8af269a69440c0308021dc92333cc"
+dependencies = [
+ "bytes",
+ "prost-derive 0.13.1",
 ]
 
 [[package]]
@@ -3935,8 +4159,29 @@ dependencies = [
  "once_cell",
  "petgraph",
  "prettyplease",
- "prost",
- "prost-types",
+ "prost 0.12.6",
+ "prost-types 0.12.6",
+ "regex",
+ "syn 2.0.66",
+ "tempfile",
+]
+
+[[package]]
+name = "prost-build"
+version = "0.13.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5bb182580f71dd070f88d01ce3de9f4da5021db7115d2e1c3605a754153b77c1"
+dependencies = [
+ "bytes",
+ "heck 0.5.0",
+ "itertools 0.13.0",
+ "log",
+ "multimap 0.10.0",
+ "once_cell",
+ "petgraph",
+ "prettyplease",
+ "prost 0.13.1",
+ "prost-types 0.13.1",
  "regex",
  "syn 2.0.66",
  "tempfile",
@@ -3955,13 +4200,35 @@ dependencies = [
  "syn 2.0.66",
 ]
 
+[[package]]
+name = "prost-derive"
+version = "0.13.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "18bec9b0adc4eba778b33684b7ba3e7137789434769ee3ce3930463ef904cfca"
+dependencies = [
+ "anyhow",
+ "itertools 0.13.0",
+ "proc-macro2",
+ "quote",
+ "syn 2.0.66",
+]
+
 [[package]]
 name = "prost-types"
 version = "0.12.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9091c90b0a32608e984ff2fa4091273cbdd755d54935c51d520887f4a1dbd5b0"
 dependencies = [
- "prost",
+ "prost 0.12.6",
+]
+
+[[package]]
+name = "prost-types"
+version = "0.13.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cee5168b05f49d4b0ca581206eb14a7b22fafd963efe729ac48eb03266e25cc2"
+dependencies = [
+ "prost 0.13.1",
 ]
 
 [[package]]
@@ -3986,9 +4253,9 @@ dependencies = [
 
 [[package]]
 name = "quick_cache"
-version = "0.5.1"
+version = "0.6.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "347e1a588d1de074eeb3c00eadff93db4db65aeb62aee852b1efd0949fe65b6c"
+checksum = "ec932c60e6faf77dc6601ea149a23d821598b019b450bb1d98fe89c0301c0b61"
 dependencies = [
  "ahash 0.8.11",
  "equivalent",
@@ -4341,6 +4608,12 @@ version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2"
 
+[[package]]
+name = "rustc-hash"
+version = "2.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "583034fd73374156e66797ed8e5b0d5690409c9226b22d87cb7f19821c05d152"
+
 [[package]]
 name = "rustc_version"
 version = "0.1.7"
@@ -4532,12 +4805,12 @@ checksum = "61697e0a1c7e512e84a621326239844a24d8207b4669b41bc18b32ea5cbf988b"
 
 [[package]]
 name = "seqrepo"
-version = "0.10.2"
+version = "0.10.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e9bad563692d6dc960f5a22a77b8efd212fdf38d2c09645246426c96ea615541"
+checksum = "8382cc8df7f9393b407caaeb2fe9ba7506a5abc32e5a117288cf9f5726c21dfb"
 dependencies = [
  "chrono",
- "noodles",
+ "noodles 0.76.0",
  "rusqlite",
  "thiserror",
  "tracing",
@@ -4598,9 +4871,9 @@ dependencies = [
 
 [[package]]
 name = "serde_with"
-version = "3.8.1"
+version = "3.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0ad483d2ab0149d5a5ebcd9972a3852711e0153d863bf5a5d0391d28883c4a20"
+checksum = "69cecfa94848272156ea67b2b1a53f20fc7bc638c4a46d2f8abde08f05f4b857"
 dependencies = [
  "base64 0.22.1",
  "chrono",
@@ -4616,9 +4889,9 @@ dependencies = [
 
 [[package]]
 name = "serde_with_macros"
-version = "3.8.1"
+version = "3.9.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "65569b702f41443e8bc8bbb1c5779bd0450bbe723b56198980e80ec45780bce2"
+checksum = "a8fee4991ef4f274617a51ad4af30519438dacb2f56ac773b08a1922ff743350"
 dependencies = [
  "darling",
  "proc-macro2",
@@ -5268,6 +5541,12 @@ version = "0.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e4259d9d4425d9f0661581b804cb85fe66a4c631cadd8f490d1c13a35d5d9291"
 
+[[package]]
+name = "unicode-segmentation"
+version = "1.11.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d4c87d22b6e3f4a18d4d40ef354e97c90fcb14dd91d7dc0aa9d8a1172ebf7202"
+
 [[package]]
 name = "unicode-width"
 version = "0.1.13"
@@ -5349,7 +5628,7 @@ dependencies = [
  "aws-config",
  "aws-sdk-s3",
  "base16ct 0.2.0",
- "bio",
+ "bio 1.6.0",
  "biocommons-bioutils",
  "byte-unit",
  "byteorder",
@@ -5376,14 +5655,14 @@ dependencies = [
  "log",
  "mehari",
  "multimap 0.10.0",
- "noodles",
- "pbjson",
- "pbjson-build",
- "pbjson-types",
+ "noodles 0.77.0",
+ "pbjson 0.6.0",
+ "pbjson-build 0.6.2",
+ "pbjson-types 0.6.0",
  "pretty_assertions",
  "procfs",
- "prost",
- "prost-build",
+ "prost 0.13.1",
+ "prost-build 0.12.6",
  "rand",
  "rand_core",
  "rayon",
@@ -5539,6 +5818,16 @@ dependencies = [
  "wasm-bindgen",
 ]
 
+[[package]]
+name = "web-time"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5a6580f308b1fad9207618087a65c04e7a10bc77e02c8e84e9b00dd4b12fa0bb"
+dependencies = [
+ "js-sys",
+ "wasm-bindgen",
+]
+
 [[package]]
 name = "whoami"
 version = "1.5.1"
diff --git a/Cargo.toml b/Cargo.toml
index f0e89a7c..d1e6d7e5 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -12,7 +12,7 @@ rust-version = "1.70.0"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-annonars = "0.39"
+annonars = "0.40"
 anyhow = "1.0"
 async-compression = { version = "0.4", features = ["tokio", "gzip"] }
 aws-sdk-s3 = { version = "1.38", features = ["behavior-version-latest"] }
@@ -35,16 +35,16 @@ ext-sort = { version = "0.1", features = ["memory-limit", "bytesize"] }
 fastrand = "2.0"
 flate2 = "1.0"
 futures = "0.3.30"
-hgvs = "0.16"
+hgvs = "0.17"
 indexmap = { version = "2.2", features = ["serde"] }
 itertools = "0.13"
 log = "0.4"
-mehari = "0.25.6"
+mehari = "0.26.0"
 multimap = "0.10"
 pbjson = "0.6"
 pbjson-types = "0.6"
 procfs = "0.16"
-prost = "0.12"
+prost = "0.13.1"
 rand = "0.8"
 rand_core = "0.6"
 rayon = "1.10"
@@ -66,7 +66,7 @@ tracing-subscriber = "0.3"
 uuid = { version = "1.9", features = ["v4", "fast-rng", "serde"] }
 
 [dependencies.noodles]
-version = "0.76.0"
+version = "0.77.0"
 features = ["bgzf", "core", "csi", "tabix", "vcf", "bcf"]
 
 
diff --git a/build.rs b/build.rs
index cc57b78e..08da62c0 100644
--- a/build.rs
+++ b/build.rs
@@ -9,7 +9,7 @@ fn main() -> Result<(), anyhow::Error> {
         "varfish/v1/clinvar.proto",
         "varfish/v1/sv.proto",
         "varfish/v1/worker.proto",
-        "varfish/v1/query_seqvars.proto",
+        "varfish/v1/seqvars/query.proto",
     ]
     .iter()
     .map(|f| root.join(f))
diff --git a/protos/varfish/v1/query_seqvars.proto b/protos/varfish/v1/query_seqvars.proto
deleted file mode 100644
index c5f4941d..00000000
--- a/protos/varfish/v1/query_seqvars.proto
+++ /dev/null
@@ -1,251 +0,0 @@
-syntax = "proto3";
-
-package varfish.v1.seqvars;
-
-
-// The Variant consequence
-enum Consequence {
-    // high impact    
-    ChromosomeNumberVariation = 0;
-    ExonLossVariant = 1;
-    FrameshiftVariant = 2;
-    RareAminoAcidVariant = 3;
-    SpliceAcceptorVariant = 4;
-    SpliceDonorVariant = 5;
-    StartLost = 6;
-    StopGained = 7;
-    StopLost = 8;
-    TranscriptAblation = 9;
-    // moderate impact
-    ThreePrimeUtrTruncation = 10;
-    FivePrimeUtrTruncaction = 11;
-    ConservativeInframeDeletion = 12;
-    ConservativeInframeInsertion = 13;
-    DisruptiveInframeDeletion = 14;
-    DisruptiveInframeInsertion = 15;
-    MissenseVariant = 16;
-    RegulatoryRegionAblation = 17;
-    SpliceRegionVariant = 18;
-    TbfsAblation = 19;
-    // low impact
-    FivePrimeUtrPrematureStartCodonGainVariant = 20;
-    InitiatorCodonVariant = 21;
-    StartRetained = 22;
-    StopRetainedVariant = 23;
-    SynonymousVariant = 24;
-    // modifier
-    ThreePrimeUtrVariant = 25;
-    FivePrimeUtrVariant = 26;
-    CodingSequenceVariant = 27;
-    ConservedIntergenicVariant = 28;
-    ConservedIntronVariant = 29;
-    DownstreamGeneVariant = 30;
-    ExonVariant = 31;
-    FeatureElongation = 32;
-    FeatureTruncation = 33;
-    GeneVariant = 34;
-    IntergenicVariant = 35;
-    IntronVariant = 36;
-    MatureMirnaVariant = 37;
-    // miRNA
-    Mirna = 38;
-    NmdTranscriptVariant = 39;
-    NonCodingTranscriptExonVariant = 40;
-    NonCodingTranscriptIntronVariant = 41;
-    RegulatoryRegionAmplification = 42;
-    RegulatoryRegionVariant = 43;
-    TfBindingSiteVariant = 44;
-    TfbsAmplification = 45;
-    TranscriptAmplification = 46;
-    TranscriptVariant = 47;
-    UpstreamGeneVariant = 48;
-}
-
-// Enumeration for recessive mode queries.
-enum RecesssiveMode {
-    Unknown = 0;
-    Recessive = 1;
-    CompoundRecessive = 2;
-}
-
-// Choice for genotype.
-enum GenotypeChoice {
-    // Any genotype
-    Any = 0;
-    // Ref. genotype
-    Ref = 1;
-    // Het. genotype
-    Het = 2;
-    // Hom. genotype
-    Hom = 3;
-    // Non-hom genotype
-    NonHom = 4;
-    // Variant genotype
-    Variant = 5;
-    // Index in comp. het. recessive inheritance
-    ComphetIndex = 6;
-    // Index in recessive inheritance
-    RecessiveIndex = 7;
-    // Parent in recessive inheritance
-    RecessiveParent = 8;
-}
-
-// Quality settings for one sample.
-message SampleQualitySettings {
-    // Drop whole variant on failure
-    bool filter_active = 1;
-    // Name of the sample filtered for
-    string sample = 2;
-    // Enable filter for sample.
-    bool enabled = 3;
-    // Minimal coverage for het. sites
-    optional int32 dp_het = 4;
-    // Minimal coverage for hom. sites
-    optional int32 dp_hom = 5;
-    // Minimal genotype quality
-    optional int32 gq = 6;
-    // Minimal allele balance for het. variants
-    optional float ab = 7;
-    // Minimal number of alternate reads
-    optional int32 ad = 8;
-    // Maximal number of alternate reads
-    optional int32 ad_max = 9;
-}
-
-message Range {
-    int32 start = 1;
-    int32 end = 2;
-}
-
-message GenomicRegion {
-    // Chromosome
-    string chrom = 1;
-    // Range of region
-    optional Range range = 2;
-}
-
-message ClinVarOptions {
-    // Wether to require ClinVar membership
-    bool require_in_clinvar = 1;
-    // Whether to include benign ClinVar variants
-    bool include_benign = 2;
-    // Whether to include pathogenic ClinVar variants
-    bool include_pathogenic = 3;
-    // Whether to include likely benign ClinVar variants
-    bool include_likely_benign = 4;
-    // Whether to include likely pathogenic ClinVar variants
-    bool include_likely_pathogenic = 5;
-    // Whether to include uncertain significance ClinVar variants
-    bool include_uncertain_significance = 6;
-    // Whether to include conflicting interpretation ClinVar variants
-    bool include_conflicting_classifications = 7;
-}
-
-
-
-message InhouseFrequencyOptions {
-    // Whether to enable filtration by 1000 Genomes.
-    bool enabled = 1;
-    // Maximal number of in-house carriers
-    optional int32 carriers = 2;
-    // Maximal number of in-house heterozygous carriers
-    optional int32 heterozygous = 3;
-    // Maximal number of in-house homozygous carriers
-    optional int32 homozygous = 4;
-    // Maximal number of in-house hemizygous carriers
-    optional int32 hemizygous = 5;
-}
-
-message GnomadNuclearOptions {
-    // Whether to enable filtration by 1000 Genomes.
-    bool enabled = 1;
-    // Maximal number of in-house carriers
-    optional int32 carriers = 2;
-    // Maximal number of in-house heterozygous carriers
-    optional int32 heterozygous = 3;
-    // Maximal number of in-house homozygous carriers
-    optional int32 homozygous = 4;
-    // Maximal number of in-house hemizygous carriers
-    optional int32 hemizygous = 5;
-    // Maximal allele frequency.
-    optional float allele_frequency = 6;
-}
-
-
-message GnomadMitochondrialOptions {
-    // Whether to enable filtration by 1000 Genomes.
-    bool enabled = 1;
-    // Maximal number of carriers
-    optional int32 carriers = 2;
-    // Maximal number of heteroplasmic carriers.
-    optional int32 heteroplasmic = 3;
-    // Maximal number of homoplasmic carriers.
-    optional int32 homoplasmic = 4;
-    // Maximal allele frequency.
-    optional float allele_frequency = 5;
-}
-
-message HelixMtDbOptions {
-    // Whether to enable filtration by mtDB
-    bool enabled = 1;
-    // Maximal frequency in HelixMtDb
-    optional float frequency = 2;
-    // Maximal number of heterozygous carriers in HelixMtDb
-    optional int32 heteroplasmic = 3;
-    // Maximal number of homozygous carriers in HelixMtDb
-    optional int32 homoplasmic = 4;
-}
-
-message PopulationFrequencyOptions {
-    // gnomAD-exomes filter
-    GnomadNuclearOptions gnomad_exomes = 1;
-    // gnomAD-genomes filter
-    GnomadNuclearOptions gnomad_genomes = 2;
-    // gnomAD-MT filter
-    GnomadMitochondrialOptions gnomad_mt = 3;
-    // HelixMtDb filter
-    HelixMtDbOptions helixmtdb = 4;
-}
-
-message VariantTypeOptions {
-    // Whether to include SNVs
-    bool snv = 1;
-    // Whether to include indels
-    bool indel = 2;
-    // Whether to include MNVs
-    bool mnv = 3;
-}
-
-message LocusRelatedOptions {
-    // List of HGNC symbols, HGNC:<ID>s, ENSG<ID>s, or NCBI Gene IDs to restrict the resulting variants to
-    repeated string gene_allowlist = 1;
-    // List of genomic regions to limit restrict the resulting variants to
-    repeated GenomicRegion genomic_regions = 2;
-}
-
-message TranscriptOptions {
-    // Whether to include coding transcripts
-    bool transcripts_coding = 1;
-    // Whether to include non-coding transcripts
-    bool transcripts_noncoding = 2;
-    // Maximal distance to next exon, if any
-    optional int32 max_exon_dist = 3;
-}
-
-message CaseQuery {
-    // Molecular consequences to consider
-    repeated Consequence consequences = 1;
-    // Quality settings for each individual
-    map<string, SampleQualitySettings> quality = 2;
-    // Genotype choice for each individual
-    map<string, GenotypeChoice> genotype = 3;
-    TranscriptOptions transcript = 4;
-    VariantTypeOptions var_type = 5;
-    LocusRelatedOptions locus = 6;
-    // ClinVar related filter options
-    // need to explicitly have an enable function
-    ClinVarOptions clinvar = 7;
-    // PopulationFrequency related filter options
-    PopulationFrequencyOptions population_frequency = 8;
-    InhouseFrequencyOptions inhouse = 9;
-}
\ No newline at end of file
diff --git a/protos/varfish/v1/seqvars/query.proto b/protos/varfish/v1/seqvars/query.proto
new file mode 100644
index 00000000..ae7418fc
--- /dev/null
+++ b/protos/varfish/v1/seqvars/query.proto
@@ -0,0 +1,341 @@
+syntax = "proto3";
+
+package varfish.v1.seqvars.query;
+
+// Enumeration for recessive mode queries.
+enum RecessiveMode {
+  // Unknown recessive mode.
+  RECESSIVE_MODE_UNSPECIFIED = 0;
+  // Disabled recessive mode.
+  RECESSIVE_MODE_DISABLED = 1;
+  // Compound heterozygous recessive mode.
+  RECESSIVE_MODE_COMPOUND_HETEROZYGOUS = 2;
+  // Homozygous recessive mode.
+  RECESSIVE_MODE_HOMOZYGOUS = 3;
+  // Generic recessive mode.
+  RECESSIVE_MODE_ANY = 4;
+}
+
+// Choice for genotype.
+enum GenotypeChoice {
+  // Unknown genotype.
+  GENOTYPE_CHOICE_UNSPECIFIED = 0;
+  // Any genoype.
+  GENOTYPE_CHOICE_ANY = 1;
+  // Reference genotype.
+  GENOTYPE_CHOICE_REF = 2;
+  // Heterozygous genotype.
+  GENOTYPE_CHOICE_HET = 3;
+  // Homozygous genotype.
+  GENOTYPE_CHOICE_HOM = 4;
+  // Non-heterozygous genotype.
+  GENOTYPE_CHOICE_NON_HET = 5;
+  // Non-homozygous genotype.
+  GENOTYPE_CHOICE_NON_HOM = 6;
+  // Variant genotype.
+  GENOTYPE_CHOICE_VARIANT = 7;
+  // Recessive index.
+  GENOTYPE_CHOICE_RECESSIVE_INDEX = 8;
+  // Recessive parent.
+  GENOTYPE_CHOICE_RECESSIVE_PARENT = 9;
+}
+
+// Genotype choice for one sample.
+message SampleGenotypeChoice {
+  // Name of the sample filtered for
+  string sample = 1;
+  // Genotype choice
+  GenotypeChoice genotype = 2;
+  // Whether to include no-call (will disable quality filter).
+  bool include_no_call = 3;
+  // Whether to enable sample in filtration
+  bool enabled = 4;
+}
+
+// Genotype-related filter settings.
+message QuerySettingsGenotype {
+  // Recessive mode
+  RecessiveMode recessive_mode = 1;
+  // List of sample genotype choices
+  repeated SampleGenotypeChoice sample_genotypes = 2;
+}
+
+// Quality settings for one sample.
+message SampleQualitySettings {
+  // Name of the sample filtered for
+  string sample = 1;
+  // Drop whole variant on failure
+  bool filter_active = 2;
+  // Minimal coverage for het. sites
+  optional int32 min_dp_het = 3;
+  // Minimal coverage for hom. sites
+  optional int32 min_dp_hom = 4;
+  // Minimal genotype quality
+  optional int32 min_gq = 5;
+  // Minimal allele balance for het. variants
+  optional float min_ab = 6;
+  // Minimal number of alternate reads
+  optional int32 min_ad = 7;
+  // Maximal number of alternate reads
+  optional int32 max_ad = 8;
+}
+
+// Per-sample quality filter settings.
+message QuerySettingsQuality {
+  // List of sample quality settings
+  repeated SampleQualitySettings sample_qualities = 1;
+}
+
+// gnomAD nuclear filter options.
+message GnomadNuclearFreqyencySettings {
+  // Whether to enable filtration by 1000 Genomes.
+  bool enabled = 1;
+  // Maximal number of in-house heterozygous carriers
+  optional int32 heterozygous = 2;
+  // Maximal number of in-house homozygous carriers
+  optional int32 homozygous = 3;
+  // Maximal number of in-house hemizygous carriers
+  optional int32 hemizygous = 4;
+  // Maximal allele frequency.
+  optional float frequency = 5;
+}
+
+// gnomAD mitochondrial filter options.
+message GnomadMitochondrialFrequencySettings {
+  // Whether to enable filtration by 1000 Genomes.
+  bool enabled = 1;
+  // Maximal number of heteroplasmic carriers.
+  optional int32 heteroplasmic = 2;
+  // Maximal number of homoplasmic carriers.
+  optional int32 homoplasmic = 3;
+  // Maximal allele frequency.
+  optional float frequency = 4;
+}
+
+// HelixMtDb filter options.
+message HelixMtDbFrequencySettings {
+  // Whether to enable filtration by mtDB
+  bool enabled = 1;
+  // Maximal number of heterozygous carriers in HelixMtDb
+  optional int32 heteroplasmic = 2;
+  // Maximal number of homozygous carriers in HelixMtDb
+  optional int32 homoplasmic = 3;
+  // Maximal frequency in HelixMtDb
+  optional float frequency = 4;
+}
+
+// In-house frequency filter options.
+message InhouseFrequencySettings {
+  // Whether to enable filtration by 1000 Genomes.
+  bool enabled = 1;
+  // Maximal number of in-house heterozygous carriers
+  optional int32 heterozygous = 2;
+  // Maximal number of in-house homozygous carriers
+  optional int32 homozygous = 3;
+  // Maximal number of in-house hemizygous carriers
+  optional int32 hemizygous = 4;
+  // Maximal number of in-house carriers
+  optional int32 carriers = 5;
+}
+
+// Population frequency filter options.
+message QuerySettingsFrequency {
+  // gnomAD-exomes filter
+  GnomadNuclearFreqyencySettings gnomad_exomes = 1;
+  // gnomAD-genomes filter
+  GnomadNuclearFreqyencySettings gnomad_genomes = 2;
+  // gnomAD-MT filter
+  GnomadMitochondrialFrequencySettings gnomad_mt = 3;
+  // HelixMtDb filter
+  HelixMtDbFrequencySettings helixmtdb = 4;
+  // In-house filter
+  InhouseFrequencySettings inhouse = 5;
+}
+
+// The variant types.
+enum VariantType {
+  // Unknown variant type
+  VARIANT_TYPE_UNSPECIFIED = 0;
+  // SNV
+  VARIANT_TYPE_SNV = 1;
+  // Indel
+  VARIANT_TYPE_INDEL = 2;
+  // MNV
+  VARIANT_TYPE_MNV = 3;
+  // Complex Substitution
+  VARIANT_TYPE_COMPLEX_SUBSTITUTION = 4;
+}
+
+// Transcript types to consider.
+enum TranscriptType {
+  // Unknown transcript type.
+  TRANSCRIPT_TYPE_UNSPECIFIED = 0;
+  // Coding transcript.
+  TRANSCRIPT_TYPE_CODING = 1;
+  // Non-coding transcript.
+  TRANSCRIPT_TYPE_NON_CODING = 2;
+}
+
+// The Variant consequence
+enum Consequence {
+  // Unknown consequence.
+  CONSEQUENCE_UNSPECIFIED = 0;
+  /*
+   * high impact
+   */
+  // Transcript ablation.
+  CONSEQUENCE_TRANSCRIPT_ABLATION = 1;
+  // Exon loss variant.
+  CONSEQUENCE_EXON_LOSS_VARIANT = 2;
+  // Splice acceptor variant
+  CONSEQUENCE_SPLICE_ACCEPTOR_VARIANT = 3;
+  // Splice donor variant
+  CONSEQUENCE_SPLICE_DONOR_VARIANT = 4;
+  // Stop gained
+  CONSEQUENCE_STOP_GAINED = 5;
+  // Frameshift variant
+  CONSEQUENCE_FRAMESHIFT_VARIANT = 6;
+  // Stop lost
+  CONSEQUENCE_STOP_LOST = 7;
+  // Start lost
+  CONSEQUENCE_START_LOST = 8;
+  // Transcript amplification
+  CONSEQUENCE_TRANSCRIPT_AMPLIFICATION = 9;
+  /*
+   * moderate impact
+   */
+  // Disruptive inframe insertion
+  CONSEQUENCE_DISRUPTIVE_INFRAME_INSERTION = 10;
+  // Disruptive inframe deletion
+  CONSEQUENCE_DISRUPTIVE_INFRAME_DELETION = 11;
+  // Conservative inframe insertion
+  CONSEQUENCE_CONSERVATIVE_INFRAME_INSERTION = 12;
+  // Conservative inframe deletion
+  CONSEQUENCE_CONSERVATIVE_INFRAME_DELETION = 13;
+  // In-frame indel.
+  CONSEQUENCE_IN_FRAME_INDEL = 14;
+  // Missense variant
+  CONSEQUENCE_MISSENSE_VARIANT = 15;
+  /*
+   * low impact
+   */
+  // Splice donor 5th base variant.
+  CONSEQUENCE_SPLICE_DONOR_FIFTH_BASE_VARIANT = 16;
+  // Splice region variant.
+  CONSEQUENCE_SPLICE_REGION_VARIANT = 17;
+  // Splice donor region variant.
+  CONSEQUENCE_SPLICE_DONOR_REGION_VARIANT = 18;
+  // Splice polypyrimidine tract variant.
+  CONSEQUENCE_SPLICE_POLYPYRIMIDINE_TRACT_VARIANT = 19;
+  // Start retained variant.
+  CONSEQUENCE_START_RETAINED_VARIANT = 20;
+  // Stop retained variant.
+  CONSEQUENCE_STOP_RETAINED_VARIANT = 21;
+  // Synonymous variant.
+  CONSEQUENCE_SYNONYMOUS_VARIANT = 22;
+  /*
+   * modifier
+   */
+  // Coding sequence variant.
+  CONSEQUENCE_CODING_SEQUENCE_VARIANT = 23;
+  // 5' UTR exon variant.
+  CONSEQUENCE_FIVE_PRIME_UTR_EXON_VARIANT = 24;
+  // 5' UTR intron variant.
+  CONSEQUENCE_FIVE_PRIME_UTR_INTRON_VARIANT = 25;
+  // 3' UTR exon variant.
+  CONSEQUENCE_THREE_PRIME_UTR_EXON_VARIANT = 26;
+  // 3' UTR intron variant.
+  CONSEQUENCE_THREE_PRIME_UTR_INTRON_VARIANT = 27;
+  // Non-coding transcript exon variant.
+  CONSEQUENCE_NON_CODING_TRANSCRIPT_EXON_VARIANT = 28;
+  // Non-coding transcript intron variant.
+  CONSEQUENCE_NON_CODING_TRANSCRIPT_INTRON_VARIANT = 29;
+  // Upstream gene variant.
+  CONSEQUENCE_UPSTREAM_GENE_VARIANT = 30;
+  // Downstream gene variant.
+  CONSEQUENCE_DOWNSTREAM_GENE_VARIANT = 31;
+  // Intergenic variant.
+  CONSEQUENCE_INTERGENIC_VARIANT = 32;
+  // Intron variant.
+  CONSEQUENCE_INTRON_VARIANT = 33;
+}
+
+// Consequence-related filter settings.
+message QuerySettingsConsequence {
+  // The variant types.
+  repeated VariantType variant_types = 1;
+  // The transcript types.
+  repeated TranscriptType transcript_types = 2;
+  // List of consequences to consider
+  repeated Consequence consequences = 3;
+  // Maximal distance to next exon, if any
+  optional int32 max_dist_to_exon = 4;
+}
+
+// An 1-based integer range.
+message Range {
+  // 1-based start position.
+  int32 start = 1;
+  // 1-based end position.
+  int32 end = 2;
+}
+
+// Genomic region.
+message GenomicRegion {
+  // Chromosome
+  string chrom = 1;
+  // Range of region
+  optional Range range = 2;
+}
+
+// Locus-related filter settings.
+message QuerySettingsLocus {
+  // List of HGNC identifiers for filtration to genes.
+  //
+  // The server will expand gene panels to gene lists here.
+  repeated string genes = 1;
+  // List of genomic regions to limit restrict the resulting variants to
+  repeated GenomicRegion genome_regions = 2;
+}
+
+// Enumeration of canonical ClinVar germline aggregte descriptions.
+enum ClinvarGermlineAggregateDescription {
+  // Unknown description.
+  CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_UNSPECIFIED = 0;
+  // Pathogenic.
+  CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_PATHOGENIC = 1;
+  // Likely pathogenic.
+  CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_LIKELY_PATHOGENIC = 2;
+  // Uncertain significance.
+  CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_UNCERTAIN_SIGNIFICANCE = 3;
+  // Likely benign.
+  CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_LIKELY_BENIGN = 4;
+  // Benign.
+  CLINVAR_GERMLINE_AGGREGATE_DESCRIPTION_BENIGN = 5;
+}
+
+// Clinvar-related query settings.
+message QuerySettingsClinVar {
+  // Wether to require ClinVar membership
+  bool presence_required = 1;
+  // The ClinVar germline aggregate description to include.
+  repeated ClinvarGermlineAggregateDescription germline_descriptions = 2;
+  // Whether to include conflicting interpretation ClinVar variants
+  bool allow_conflicting_interpretations = 3;
+}
+
+// Store query information for one case.
+message CaseQuery {
+  // Genotype query settings.
+  QuerySettingsGenotype genotype = 1;
+  // Quality query settings.
+  QuerySettingsQuality quality = 2;
+  // Frequency query settings.
+  QuerySettingsFrequency frequency = 3;
+  // Consequence query settings.
+  QuerySettingsConsequence consequence = 4;
+  // Locus query settings.
+  QuerySettingsLocus locus = 5;
+  // ClinVar query settings.
+  QuerySettingsClinVar clinvar = 6;
+}
diff --git a/protos/varfish/v1/worker.proto b/protos/varfish/v1/worker.proto
index b822ee68..ed6ccd3c 100644
--- a/protos/varfish/v1/worker.proto
+++ b/protos/varfish/v1/worker.proto
@@ -6,22 +6,22 @@ package varfish.v1.worker;
 
 // Protocol buffer for storing a list of file identifier mappings.
 message FileIdentifierMappings {
-    // Protocol buffer for storing file identifier mapping for one file.
-    message Mapping {
-        // Protocol buffer to store one mapping entry.
-        message Entry {
-            // Identifier as given in input file.
-            string src = 1;
-            // Identifier to use in output file.
-            string dst = 2;
-        }
-
-        // Path to the file to obtain mapping for, as given on the command line.
-        string path = 1;
-        // List of identifier mappings.
-        repeated Entry entries = 2;
+  // Protocol buffer for storing file identifier mapping for one file.
+  message Mapping {
+    // Protocol buffer to store one mapping entry.
+    message Entry {
+      // Identifier as given in input file.
+      string src = 1;
+      // Identifier to use in output file.
+      string dst = 2;
     }
 
-    // One file per mapping.
-    repeated Mapping mappings = 1;
+    // Path to the file to obtain mapping for, as given on the command line.
+    string path = 1;
+    // List of identifier mappings.
+    repeated Entry entries = 2;
+  }
+
+  // One file per mapping.
+  repeated Mapping mappings = 1;
 }
diff --git a/src/common/mod.rs b/src/common/mod.rs
index d6dd46b9..243a200e 100644
--- a/src/common/mod.rs
+++ b/src/common/mod.rs
@@ -475,8 +475,15 @@ pub fn add_contigs_38(
     Ok(builder)
 }
 
+/// Error type for `genotype_to_string()`
+#[derive(thiserror::Error, Debug, Clone)]
+pub enum GenotypeToStringError {
+    #[error("Could not convert genotype {0}: {1}")]
+    InconvertibleGenotype(String, String),
+}
+
 /// Convert genotype to String value.
-pub fn genotype_to_string<G>(gt: &G) -> Result<String, anyhow::Error>
+pub fn genotype_to_string<G>(gt: &G) -> Result<String, GenotypeToStringError>
 where
     G: vcf::variant::record::samples::series::value::Genotype + ?Sized,
 {
@@ -484,8 +491,9 @@ where
 
     let mut tmp = String::new();
     for allele in gt.iter() {
-        let (position, phasing) =
-            allele.map_err(|e| anyhow::anyhow!("problem with Genotype {:?}: {}", gt, e))?;
+        let (position, phasing) = allele.map_err(|e| {
+            GenotypeToStringError::InconvertibleGenotype(format!("{:?}", gt), format!("{}", e))
+        })?;
         // sic! VCF 4.4 has optional/implicit leading phasing indicator
         match phasing {
             Phasing::Phased => tmp.push('|'),
diff --git a/src/pbs.rs b/src/pbs.rs
index a86c866f..32a27e44 100644
--- a/src/pbs.rs
+++ b/src/pbs.rs
@@ -1,16 +1,29 @@
 //! Data structures for (de-)serialization as generated by `prost-build`.
 
+/// Code generate for protobufs by `prost-build`.
+pub mod varfish {
+    /// Code generate for protobufs by `prost-build`.
+    pub mod v1 {
+        /// Code generate for protobufs by `prost-build`.
+        pub mod seqvars {
+            /// Code generate for protobufs by `prost-build`.
+            pub mod query {
+                include!(concat!(env!("OUT_DIR"), "/varfish.v1.seqvars.query.rs"));
+                include!(concat!(
+                    env!("OUT_DIR"),
+                    "/varfish.v1.seqvars.query.serde.rs"
+                ));
+            }
+        }
+    }
+}
+
 /// Code generate for protobufs by `prost-build`.
 pub mod clinvar {
     include!(concat!(env!("OUT_DIR"), "/varfish.v1.clinvar.rs"));
     include!(concat!(env!("OUT_DIR"), "/varfish.v1.clinvar.serde.rs"));
 }
 
-pub mod seqvars {
-    include!(concat!(env!("OUT_DIR"), "/varfish.v1.seqvars.rs"));
-    include!(concat!(env!("OUT_DIR"), "/varfish.v1.seqvars.serde.rs"));
-}
-
 /// Code generate for protobufs by `prost-build`.
 pub mod svs {
     include!(concat!(env!("OUT_DIR"), "/varfish.v1.svs.rs"));
diff --git a/src/seqvars/ingest/header.rs b/src/seqvars/ingest/header.rs
index d05ae3f7..b6d828ec 100644
--- a/src/seqvars/ingest/header.rs
+++ b/src/seqvars/ingest/header.rs
@@ -291,6 +291,38 @@ pub fn build_output_header(
                 "Number of hemi. alt. carriers in gnomAD genomes",
             ),
         )
+        .add_info(
+            "gnomad_mtdna_an",
+            Map::<Info>::new(
+                Number::Count(1),
+                Type::Integer,
+                "Number of alleles in gnomAD MT",
+            ),
+        )
+        .add_info(
+            "gnomad_mtdna_hom",
+            Map::<Info>::new(
+                Number::Count(1),
+                Type::Integer,
+                "Number of hom. alt. carriers in gnomAD MT",
+            ),
+        )
+        .add_info(
+            "gnomad_mtdna_het",
+            Map::<Info>::new(
+                Number::Count(1),
+                Type::Integer,
+                "Number of het. alt. carriers in gnomAD MT",
+            ),
+        )
+        .add_info(
+            "gnomad_mtdna_hemi",
+            Map::<Info>::new(
+                Number::Count(1),
+                Type::Integer,
+                "Number of hemi. alt. carriers in gnomAD MT",
+            ),
+        )
         .add_info(
             "helix_an",
             Map::<Info>::new(
diff --git a/src/seqvars/ingest/mod.rs b/src/seqvars/ingest/mod.rs
index 2ca82e60..a77342bb 100644
--- a/src/seqvars/ingest/mod.rs
+++ b/src/seqvars/ingest/mod.rs
@@ -158,9 +158,9 @@ fn transform_format_value(
                     let gt_captures = gt_re
                         .captures(&gt)
                         .unwrap_or_else(|| panic!("FORMAT/GT cannot be parsed: {}", &gt));
-                    let gt_1 = gt_captures.get(1).expect("must be capture").as_str();
-                    let gt_2 = gt_captures.get(2).expect("must be capture").as_str();
-                    let gt_3 = gt_captures.get(3).expect("must be capture").as_str();
+                    let gt_1 = gt_captures.get(1).expect("must be captured").as_str();
+                    let gt_2 = gt_captures.get(2).expect("must be captured").as_str();
+                    let gt_3 = gt_captures.get(3).expect("must be captured").as_str();
 
                     let new_gt = format!(
                         "{}{}{}",
diff --git a/src/seqvars/query/annonars.rs b/src/seqvars/query/annonars.rs
index dcf7f9d6..2d430c23 100644
--- a/src/seqvars/query/annonars.rs
+++ b/src/seqvars/query/annonars.rs
@@ -2,11 +2,11 @@
 
 use std::{path::Path, sync::Arc};
 
-use prost::Message;
-
 use crate::{common::GenomeRelease, seqvars::ingest::path_component};
 
-use super::schema::SequenceVariant;
+use prost::Message as _;
+
+use super::schema::data::VariantRecord;
 
 /// Bundle the types needed for databases.
 pub struct AnnonarsDbs {
@@ -175,7 +175,7 @@ impl Annotator {
 
         raw_value
             .map(|raw_value| {
-                annonars::pbs::genes::base::Record::decode(&mut std::io::Cursor::new(&raw_value))
+                annonars::pbs::genes::base::Record::decode(std::io::Cursor::new(raw_value))
                     .map_err(|e| {
                         anyhow::anyhow!(
                             "problem decoding record from genes database for HGNC ID {}: {}",
@@ -194,7 +194,7 @@ impl Annotator {
     /// If there is a problem querying the database.
     pub fn query_clinvar_minimal(
         &self,
-        seqvar: &SequenceVariant,
+        seqvar: &VariantRecord,
     ) -> Result<Option<annonars::pbs::clinvar::minimal::ExtractedVcvRecordList>, anyhow::Error>
     {
         let cf_data = self
@@ -202,13 +202,7 @@ impl Annotator {
             .clinvar_db
             .cf_handle("clinvar")
             .ok_or_else(|| anyhow::anyhow!("could not get clinvar column family"))?;
-
-        let variant = annonars::common::spdi::Var::new(
-            annonars::common::cli::canonicalize(&seqvar.chrom),
-            seqvar.pos,
-            seqvar.reference.clone(),
-            seqvar.alternative.clone(),
-        );
+        let variant: annonars::common::spdi::Var = seqvar.vcf_variant.clone().into();
 
         annonars::clinvar_minimal::cli::query::query_for_variant(
             &variant,
@@ -226,20 +220,14 @@ impl Annotator {
     /// If there is a problem querying the database.
     pub fn query_dbsnp(
         &self,
-        seqvar: &SequenceVariant,
+        seqvar: &VariantRecord,
     ) -> Result<Option<annonars::dbsnp::pbs::Record>, anyhow::Error> {
         let cf_data = self
             .annonars_dbs
             .dbsnp_db
             .cf_handle("dbsnp_data")
             .ok_or_else(|| anyhow::anyhow!("could not get dbsnp_data column family"))?;
-
-        let variant = annonars::common::spdi::Var::new(
-            annonars::common::cli::canonicalize(&seqvar.chrom),
-            seqvar.pos,
-            seqvar.reference.clone(),
-            seqvar.alternative.clone(),
-        );
+        let variant: annonars::common::spdi::Var = seqvar.vcf_variant.clone().into();
 
         annonars::dbsnp::cli::query::query_for_variant(
             &variant,
@@ -257,20 +245,14 @@ impl Annotator {
     /// If there is a problem querying the database.
     pub fn query_cadd(
         &self,
-        seqvar: &SequenceVariant,
+        seqvar: &VariantRecord,
     ) -> Result<Option<Vec<serde_json::Value>>, anyhow::Error> {
         let cf_data = self
             .annonars_dbs
             .cadd_db
             .cf_handle("tsv_data")
             .ok_or_else(|| anyhow::anyhow!("could not get tsv_data column family"))?;
-
-        let variant = annonars::common::spdi::Var::new(
-            annonars::common::cli::canonicalize(&seqvar.chrom),
-            seqvar.pos,
-            seqvar.reference.clone(),
-            seqvar.alternative.clone(),
-        );
+        let variant: annonars::common::spdi::Var = seqvar.vcf_variant.clone().into();
 
         let values = annonars::tsv::cli::query::query_for_variant(
             &variant,
@@ -291,20 +273,14 @@ impl Annotator {
     /// If there is a problem querying the database.
     pub fn query_dbnsfp(
         &self,
-        seqvar: &SequenceVariant,
+        seqvar: &VariantRecord,
     ) -> Result<Option<Vec<serde_json::Value>>, anyhow::Error> {
         let cf_data = self
             .annonars_dbs
             .dbnsfp_db
             .cf_handle("tsv_data")
             .ok_or_else(|| anyhow::anyhow!("could not get tsv_data column family"))?;
-
-        let variant = annonars::common::spdi::Var::new(
-            annonars::common::cli::canonicalize(&seqvar.chrom),
-            seqvar.pos,
-            seqvar.reference.clone(),
-            seqvar.alternative.clone(),
-        );
+        let variant: annonars::common::spdi::Var = seqvar.vcf_variant.clone().into();
 
         let values = annonars::tsv::cli::query::query_for_variant(
             &variant,
diff --git a/src/seqvars/query/interpreter/clinvar.rs b/src/seqvars/query/interpreter/clinvar.rs
index 587de6b8..a2554fc5 100644
--- a/src/seqvars/query/interpreter/clinvar.rs
+++ b/src/seqvars/query/interpreter/clinvar.rs
@@ -1,15 +1,18 @@
 use crate::seqvars::query::{
     annonars::Annotator,
-    schema::{CaseQuery, SequenceVariant},
+    schema::{
+        data::VariantRecord,
+        query::{CaseQuery, ClinvarGermlineAggregateDescription},
+    },
 };
 
-/// Determine whether the `SequenceVariant` passes the clinvar filter.
+/// Determine whether the `VariantRecord` passes the clinvar filter.
 pub fn passes(
     query: &CaseQuery,
     annotator: &Annotator,
-    seqvar: &SequenceVariant,
+    seqvar: &VariantRecord,
 ) -> Result<bool, anyhow::Error> {
-    if !query.require_in_clinvar {
+    if !query.clinvar.presence_required {
         return Ok(true);
     }
 
@@ -40,20 +43,29 @@ pub fn passes(
             .cloned()
             .unwrap_or_default();
 
+        use ClinvarGermlineAggregateDescription::*;
         let result = match description.to_lowercase().as_str() {
-            "benign" => query.clinvar.include_benign,
+            "benign" => query.clinvar.germline_descriptions.contains(&Benign),
             "benign/likely benign" => {
-                query.clinvar.include_benign || query.clinvar.include_likely_benign
+                query.clinvar.germline_descriptions.contains(&Benign)
+                    || query.clinvar.germline_descriptions.contains(&LikelyBenign)
             }
-            "likely benign" => query.clinvar.include_likely_benign,
-            "pathogenic" => query.clinvar.include_pathogenic,
+            "likely benign" => query.clinvar.germline_descriptions.contains(&LikelyBenign),
+            "pathogenic" => query.clinvar.germline_descriptions.contains(&Pathogenic),
             "pathogenic/likely pathogenic" => {
-                query.clinvar.include_pathogenic || query.clinvar.include_likely_pathogenic
+                query.clinvar.germline_descriptions.contains(&LikelyBenign)
+                    || query.clinvar.germline_descriptions.contains(&Benign)
             }
-            "likely pathogenic" => query.clinvar.include_likely_pathogenic,
-            "uncertain significance" => query.clinvar.include_uncertain_significance,
+            "likely pathogenic" => query
+                .clinvar
+                .germline_descriptions
+                .contains(&LikelyPathogenic),
+            "uncertain significance" => query
+                .clinvar
+                .germline_descriptions
+                .contains(&UncertainSignificance),
             "conflicting classifications of pathogenicity" => {
-                query.clinvar.include_uncertain_significance
+                query.clinvar.allow_conflicting_interpretations
             }
             _ => {
                 // We could also downtone this to debug.
diff --git a/src/seqvars/query/interpreter/consequences.rs b/src/seqvars/query/interpreter/consequences.rs
index 2803312f..e939f808 100644
--- a/src/seqvars/query/interpreter/consequences.rs
+++ b/src/seqvars/query/interpreter/consequences.rs
@@ -1,21 +1,22 @@
-use crate::seqvars::query::schema::{CaseQuery, SequenceVariant};
+use mehari::annotate::seqvars::ann;
 
-/// Determine whether the `SequenceVariant` passes the consequences filter.
-pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result<bool, anyhow::Error> {
+use crate::seqvars::query::schema::{data::VariantRecord, query::CaseQuery};
+
+/// Determine whether the `VariantRecord` passes the consequences filter.
+pub fn passes(query: &CaseQuery, seqvar: &VariantRecord) -> Result<bool, anyhow::Error> {
     // If no consequences are specified, the variant passes.
-    if query.consequences.is_empty() {
+    if query.consequence.consequences.is_empty() {
         return Ok(true);
     }
     // Variants on chrMT always pass.
-    let chrom = annonars::common::cli::canonicalize(&seqvar.chrom);
+    let chrom = annonars::common::cli::canonicalize(&seqvar.vcf_variant.chrom);
     if chrom == "MT" {
         return Ok(true);
     }
 
-    let query_csq = std::collections::BTreeSet::from_iter(query.consequences.iter().cloned());
+    let query_csq: indexmap::IndexSet<ann::Consequence> = indexmap::IndexSet::from_iter(query.consequence.consequences.iter().cloned().map(|c| c.into()));
     for ann_field in &seqvar.ann_fields {
-        let seqvar_csq =
-            std::collections::BTreeSet::from_iter(ann_field.consequences.iter().cloned());
+        let seqvar_csq: indexmap::IndexSet<ann::Consequence> = indexmap::IndexSet::from_iter(ann_field.consequences.iter().cloned());
         let intersection_csq = query_csq.intersection(&seqvar_csq);
         if intersection_csq.count() > 0 {
             return Ok(true);
@@ -25,34 +26,47 @@ pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result<bool, anyho
     tracing::trace!(
         "variant {:?} fails consequence filter {:?}",
         &seqvar,
-        &query.consequences
+        &query.consequence
     );
     Ok(false)
 }
 
 #[cfg(test)]
 mod test {
-    use mehari::annotate::seqvars::ann::{AnnField, Consequence};
+    use mehari::annotate::seqvars::ann;
     use rstest::rstest;
     use strum::IntoEnumIterator;
 
-    use crate::seqvars::query::schema::{CaseQuery, SequenceVariant};
+    use crate::seqvars::query::schema::{
+        data::{VariantRecord, VcfVariant},
+        query::{CaseQuery, QuerySettingsConsequence},
+    };
 
     #[rstest]
     #[case(true)]
     #[case(false)]
     fn passes_consequence(#[case] c_equals_csq: bool) -> Result<(), anyhow::Error> {
-        for csq in Consequence::iter() {
+        use crate::seqvars::query::schema::query::Consequence;
+
+        for csq in ann::Consequence::iter() {
             let query = CaseQuery {
-                consequences: Consequence::iter()
-                    .filter(|c| (*c == csq) == c_equals_csq)
-                    .collect(),
+                consequence: QuerySettingsConsequence {
+                    consequences: Consequence::iter()
+                        .filter(|c| (<Consequence as Into<ann::Consequence>>::into(*c) == csq) == c_equals_csq)
+                        .collect(),
+                    ..Default::default()
+                },
                 ..Default::default()
             };
-            let seq_var = SequenceVariant {
-                reference: "G".into(),
-                alternative: "A".into(),
-                ann_fields: vec![AnnField {
+            let seq_var = VariantRecord {
+                vcf_variant: VcfVariant {
+                    chrom: "1".into(),
+                    pos: 1,
+                    ref_allele: "G".into(),
+                    alt_allele: "A".into(),
+                    ..Default::default()
+                },
+                ann_fields: vec![ann::AnnField {
                     allele: mehari::annotate::seqvars::ann::Allele::Alt {
                         alternative: "A".into(),
                     },
diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs
index 3131ab76..a507a609 100644
--- a/src/seqvars/query/interpreter/frequency.rs
+++ b/src/seqvars/query/interpreter/frequency.rs
@@ -1,69 +1,96 @@
-use crate::seqvars::query::schema::{CaseQuery, SequenceVariant};
+use crate::seqvars::query::schema::{
+    data::{Af, VariantRecord},
+    query::CaseQuery,
+};
 
-/// Determine whether the `SequenceVariant` passes the frequency filter.
-pub fn passes(query: &CaseQuery, s: &SequenceVariant) -> Result<bool, anyhow::Error> {
-    let pop = &query.population_frequency;
-    let is_mtdna = annonars::common::cli::canonicalize(&s.chrom) == "MT";
+/// Determine whether the `VariantRecord` passes the frequency filter.
+pub fn passes(query: &CaseQuery, s: &VariantRecord) -> Result<bool, anyhow::Error> {
+    let frequency = &query.frequency;
+    let is_mtdna = annonars::common::cli::canonicalize(&s.vcf_variant.chrom) == "MT";
 
     if is_mtdna {
-        if pop.helixmtdb.enabled
-            && (pop.helixmtdb.frequency.is_some()
-                && s.helixmtdb_af() > pop.helixmtdb.frequency.expect("tested before")
-                || pop.helixmtdb.heteroplasmic.is_some()
+        if frequency.helixmtdb.enabled
+            && (frequency.helixmtdb.frequency.is_some()
+                && s.population_frequencies.helixmtdb.af()
+                    > frequency.helixmtdb.frequency.expect("tested before")
+                || frequency.helixmtdb.heteroplasmic.is_some()
                     && s.population_frequencies.helixmtdb.het
-                        > pop.helixmtdb.heteroplasmic.expect("tested before")
-                || pop.helixmtdb.homoplasmic.is_some()
+                        > frequency.helixmtdb.heteroplasmic.expect("tested before")
+                || frequency.helixmtdb.homoplasmic.is_some()
                     && s.population_frequencies.helixmtdb.hom
-                        > pop.helixmtdb.homoplasmic.expect("tested before"))
+                        > frequency.helixmtdb.homoplasmic.expect("tested before"))
         {
             tracing::trace!(
                 "variant {:?} fails HelixMtDb frequency filter {:?}",
                 s,
-                &pop
+                &frequency.helixmtdb
+            );
+            return Ok(false);
+        }
+        if frequency.gnomad_mt.enabled
+            && (frequency.gnomad_mt.frequency.is_some()
+                && s.population_frequencies.gnomad_mt.af()
+                    > frequency.gnomad_mt.frequency.expect("tested before")
+                || frequency.gnomad_mt.heteroplasmic.is_some()
+                    && s.population_frequencies.gnomad_mt.het
+                        > frequency.gnomad_mt.heteroplasmic.expect("tested before")
+                || frequency.gnomad_mt.homoplasmic.is_some()
+                    && s.population_frequencies.gnomad_mt.hom
+                        > frequency.gnomad_mt.homoplasmic.expect("tested before"))
+        {
+            tracing::trace!(
+                "variant {:?} fails gnomAD-MT frequency filter {:?}",
+                s,
+                &frequency.gnomad_mt
+            );
+            return Ok(false);
+        }
+    } else {
+        if frequency.gnomad_exomes.enabled
+            && (frequency.gnomad_exomes.frequency.is_some()
+                && s.population_frequencies.gnomad_exomes.af()
+                    > frequency.gnomad_exomes.frequency.expect("tested before")
+                || frequency.gnomad_exomes.heterozygous.is_some()
+                    && s.population_frequencies.gnomad_exomes.het
+                        > frequency.gnomad_exomes.heterozygous.expect("tested before")
+                || frequency.gnomad_exomes.homozygous.is_some()
+                    && s.population_frequencies.gnomad_exomes.hom
+                        > frequency.gnomad_exomes.homozygous.expect("tested before")
+                || frequency.gnomad_exomes.hemizygous.is_some()
+                    && s.population_frequencies.gnomad_exomes.hemi
+                        > frequency.gnomad_exomes.hemizygous.expect("tested before"))
+        {
+            tracing::trace!(
+                "variant {:?} fails gnomAD-exomes frequency filter {:?}",
+                s,
+                &frequency.gnomad_exomes
+            );
+            return Ok(false);
+        }
+        if frequency.gnomad_genomes.enabled
+            && (frequency.gnomad_genomes.frequency.is_some()
+                && s.population_frequencies.gnomad_genomes.af()
+                    > frequency.gnomad_genomes.frequency.expect("tested before")
+                || frequency.gnomad_genomes.heterozygous.is_some()
+                    && s.population_frequencies.gnomad_genomes.het
+                        > frequency
+                            .gnomad_genomes
+                            .heterozygous
+                            .expect("tested before")
+                || frequency.gnomad_genomes.homozygous.is_some()
+                    && s.population_frequencies.gnomad_genomes.hom
+                        > frequency.gnomad_genomes.homozygous.expect("tested before")
+                || frequency.gnomad_genomes.hemizygous.is_some()
+                    && s.population_frequencies.gnomad_genomes.hemi
+                        > frequency.gnomad_genomes.hemizygous.expect("tested before"))
+        {
+            tracing::trace!(
+                "variant {:?} fails gnomAD-genomes frequency filter {:?}",
+                s,
+                &frequency.gnomad_genomes
             );
             return Ok(false);
         }
-    } else if pop.gnomad_exomes.enabled
-        && (pop.gnomad_exomes.allele_frequency.is_some()
-            && s.gnomad_exomes_af() > pop.gnomad_exomes.allele_frequency.expect("tested before")
-            || pop.gnomad_exomes.heterozygous.is_some()
-                && s.population_frequencies.gnomad.exomes_het
-                    > pop.gnomad_exomes.heterozygous.expect("tested before")
-            || pop.gnomad_exomes.homozygous.is_some()
-                && s.population_frequencies.gnomad.exomes_hom
-                    > pop.gnomad_exomes.homozygous.expect("tested before")
-            || pop.gnomad_exomes.hemizygous.is_some()
-                && s.population_frequencies.gnomad.exomes_hemi
-                    > pop.gnomad_exomes.hemizygous.expect("tested before"))
-    {
-        tracing::trace!(
-            "variant {:?} fails gnomAD exomes frequency filter {:?}",
-            s,
-            &pop.gnomad_exomes.allele_frequency
-        );
-        return Ok(false);
-    }
-
-    if pop.gnomad_genomes.enabled
-        && (pop.gnomad_genomes.allele_frequency.is_some()
-            && s.gnomad_genomes_af() > pop.gnomad_genomes.allele_frequency.expect("tested before")
-            || pop.gnomad_genomes.heterozygous.is_some()
-                && s.population_frequencies.gnomad.genomes_het
-                    > pop.gnomad_genomes.heterozygous.expect("tested before")
-            || pop.gnomad_genomes.homozygous.is_some()
-                && s.population_frequencies.gnomad.genomes_hom
-                    > pop.gnomad_genomes.homozygous.expect("tested before")
-            || !is_mtdna
-                && pop.gnomad_genomes.hemizygous.is_some()
-                && s.population_frequencies.gnomad.genomes_hemi
-                    > pop.gnomad_genomes.hemizygous.expect("tested before"))
-    {
-        tracing::trace!(
-            "variant {:?} fails gnomAD genomes allele_frequency filter {:?}",
-            s,
-            &pop.gnomad_genomes.allele_frequency
-        );
-        return Ok(false);
     }
 
     Ok(true)
@@ -76,7 +103,14 @@ mod test {
     use rstest::rstest;
 
     use crate::seqvars::query::schema::{
-        CaseQuery, HelixMtDBs, PopulationFrequencies, SequenceVariant,
+        data::{
+            MitochondrialFrequencies, NuclearFrequencies, PopulationFrequencies, VariantRecord,
+            VcfVariant,
+        },
+        query::{
+            CaseQuery, GnomadNuclearFrequencySettings, HelixMtDbFrequencySettings,
+            QuerySettingsFrequency,
+        },
     };
 
     #[rstest]
@@ -144,15 +178,11 @@ mod test {
         #[case] query_gnomad_exomes_hemizygous: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::{
-            GnomadNuclearOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
-        };
-
         let query = CaseQuery {
-            population_frequency: PopulationFrequencyOptions {
-                gnomad_exomes: GnomadNuclearOptions {
+            frequency: QuerySettingsFrequency {
+                gnomad_exomes: GnomadNuclearFrequencySettings {
                     enabled: query_gnomad_exomes_enabled,
-                    allele_frequency: query_gnomad_exomes_frequency,
+                    frequency: query_gnomad_exomes_frequency,
                     heterozygous: query_gnomad_exomes_heterozygous,
                     homozygous: query_gnomad_exomes_homozygous,
                     hemizygous: query_gnomad_exomes_hemizygous,
@@ -162,20 +192,23 @@ mod test {
             },
             ..Default::default()
         };
-        let seq_var = SequenceVariant {
+        let seq_var = VariantRecord {
             population_frequencies: PopulationFrequencies {
-                gnomad: Gnomads {
-                    exomes_an: seqvar_gnomad_exomes_an,
-                    exomes_het: seqvar_gnomad_exomes_het,
-                    exomes_hom: seqvar_gnomad_exomes_hom,
-                    exomes_hemi: seqvar_gnomad_exomes_hemi,
+                gnomad_exomes: NuclearFrequencies {
+                    an: seqvar_gnomad_exomes_an,
+                    het: seqvar_gnomad_exomes_het,
+                    hom: seqvar_gnomad_exomes_hom,
+                    hemi: seqvar_gnomad_exomes_hemi,
                     ..Default::default()
                 },
                 ..Default::default()
             },
-            chrom: "X".to_string(),
-            reference: "G".into(),
-            alternative: "A".into(),
+            vcf_variant: VcfVariant {
+                chrom: "X".to_string(),
+                pos: 1,
+                ref_allele: "G".into(),
+                alt_allele: "A".into(),
+            },
             ann_fields: vec![AnnField {
                 allele: mehari::annotate::seqvars::ann::Allele::Alt {
                     alternative: "A".into(),
@@ -187,6 +220,7 @@ mod test {
                 feature_type: mehari::annotate::seqvars::ann::FeatureType::SoTerm {
                     term: mehari::annotate::seqvars::ann::SoFeature::Transcript,
                 },
+                strand: Default::default(),
                 feature_id: Default::default(),
                 feature_biotype: vec![mehari::annotate::seqvars::ann::FeatureBiotype::Coding],
                 rank: Default::default(),
@@ -271,15 +305,11 @@ mod test {
         #[case] query_gnomad_genomes_hemizygous: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::{
-            GnomadNuclearOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
-        };
-
         let query = CaseQuery {
-            population_frequency: PopulationFrequencyOptions {
-                gnomad_genomes: GnomadNuclearOptions {
+            frequency: QuerySettingsFrequency {
+                gnomad_genomes: GnomadNuclearFrequencySettings {
                     enabled: query_gnomad_genomes_enabled,
-                    allele_frequency: query_gnomad_genomes_frequency,
+                    frequency: query_gnomad_genomes_frequency,
                     heterozygous: query_gnomad_genomes_heterozygous,
                     homozygous: query_gnomad_genomes_homozygous,
                     hemizygous: query_gnomad_genomes_hemizygous,
@@ -289,20 +319,23 @@ mod test {
             },
             ..Default::default()
         };
-        let seq_var = SequenceVariant {
+        let seq_var = VariantRecord {
             population_frequencies: PopulationFrequencies {
-                gnomad: Gnomads {
-                    genomes_an: seqvar_gnomad_genomes_an,
-                    genomes_het: seqvar_gnomad_genomes_het,
-                    genomes_hom: seqvar_gnomad_genomes_hom,
-                    genomes_hemi: seqvar_gnomad_genomes_hemi,
+                gnomad_genomes: NuclearFrequencies {
+                    an: seqvar_gnomad_genomes_an,
+                    het: seqvar_gnomad_genomes_het,
+                    hom: seqvar_gnomad_genomes_hom,
+                    hemi: seqvar_gnomad_genomes_hemi,
                     ..Default::default()
                 },
                 ..Default::default()
             },
-            chrom: "X".to_string(),
-            reference: "G".into(),
-            alternative: "A".into(),
+            vcf_variant: VcfVariant {
+                chrom: "X".to_string(),
+                pos: 1,
+                ref_allele: "G".into(),
+                alt_allele: "A".into(),
+            },
             ann_fields: vec![AnnField {
                 allele: mehari::annotate::seqvars::ann::Allele::Alt {
                     alternative: "A".into(),
@@ -314,6 +347,7 @@ mod test {
                 feature_type: mehari::annotate::seqvars::ann::FeatureType::SoTerm {
                     term: mehari::annotate::seqvars::ann::SoFeature::Transcript,
                 },
+                strand: Default::default(),
                 feature_id: Default::default(),
                 feature_biotype: vec![mehari::annotate::seqvars::ann::FeatureBiotype::Coding],
                 rank: Default::default(),
@@ -373,38 +407,39 @@ mod test {
         #[case] seqvar_helix_an: i32,
         #[case] seqvar_helix_het: i32,
         #[case] seqvar_helix_hom: i32,
-        #[case] query_helix_enabled: bool,
-        #[case] query_helix_frequency: Option<f32>,
-        #[case] query_helix_heteroplasmic: Option<i32>,
-        #[case] query_helix_homoplasmic: Option<i32>,
+        #[case] query_helixmtdb_enabled: bool,
+        #[case] query_helixmtdb_frequency: Option<f32>,
+        #[case] query_helixmtdb_heteroplasmic: Option<i32>,
+        #[case] query_helixmtdb_homoplasmic: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::{HelixMtDbOptions, PopulationFrequencyOptions};
-
         let query = CaseQuery {
-            population_frequency: PopulationFrequencyOptions {
-                helixmtdb: HelixMtDbOptions {
-                    enabled: query_helix_enabled,
-                    frequency: query_helix_frequency,
-                    heteroplasmic: query_helix_heteroplasmic,
-                    homoplasmic: query_helix_homoplasmic,
+            frequency: QuerySettingsFrequency {
+                helixmtdb: HelixMtDbFrequencySettings {
+                    enabled: query_helixmtdb_enabled,
+                    frequency: query_helixmtdb_frequency,
+                    heteroplasmic: query_helixmtdb_heteroplasmic,
+                    homoplasmic: query_helixmtdb_homoplasmic,
                 },
                 ..Default::default()
             },
             ..Default::default()
         };
-        let seq_var = SequenceVariant {
+        let seq_var = VariantRecord {
             population_frequencies: PopulationFrequencies {
-                helixmtdb: HelixMtDBs {
+                helixmtdb: MitochondrialFrequencies {
                     an: seqvar_helix_an,
                     het: seqvar_helix_het,
                     hom: seqvar_helix_hom,
                 },
                 ..Default::default()
             },
-            chrom: "MT".to_string(),
-            reference: "G".into(),
-            alternative: "A".into(),
+            vcf_variant: VcfVariant {
+                chrom: "MT".to_string(),
+                pos: 1,
+                ref_allele: "G".into(),
+                alt_allele: "A".into(),
+            },
             ann_fields: vec![AnnField {
                 allele: mehari::annotate::seqvars::ann::Allele::Alt {
                     alternative: "A".into(),
@@ -416,6 +451,7 @@ mod test {
                 feature_type: mehari::annotate::seqvars::ann::FeatureType::SoTerm {
                     term: mehari::annotate::seqvars::ann::SoFeature::Transcript,
                 },
+                strand: Default::default(),
                 feature_id: Default::default(),
                 feature_biotype: vec![mehari::annotate::seqvars::ann::FeatureBiotype::Coding],
                 rank: Default::default(),
@@ -472,46 +508,45 @@ mod test {
     // hom. count: pass (fail but filter is disabled)
     #[case(1000, 0, 2, false, None, None, Some(1), true)]
     #[allow(clippy::too_many_arguments)]
-    fn passes_frequency_gnomad_genomes_chrmt(
+    fn passes_frequency_gnomad_mtdna(
         #[case] seqvar_gnomad_genomes_an: i32,
         #[case] seqvar_gnomad_genomes_het: i32,
         #[case] seqvar_gnomad_genomes_hom: i32,
-        #[case] query_gnomad_genomes_enabled: bool,
-        #[case] query_gnomad_genomes_frequency: Option<f32>,
-        #[case] query_gnomad_genomes_heteroplasmic: Option<i32>,
-        #[case] query_gnomad_genomes_homoplasmic: Option<i32>,
+        #[case] query_gnomad_mtdna_enabled: bool,
+        #[case] query_gnomad_mtdna_frequency: Option<f32>,
+        #[case] query_gnomad_mtdna_heteroplasmic: Option<i32>,
+        #[case] query_gnomad_mtdna_homoplasmic: Option<i32>,
         #[case] expected_pass_all: bool,
     ) -> Result<(), anyhow::Error> {
-        use crate::seqvars::query::schema::{
-            GnomadNuclearOptions, Gnomads, PopulationFrequencies, PopulationFrequencyOptions,
-        };
-
         let query = CaseQuery {
-            population_frequency: PopulationFrequencyOptions {
-                gnomad_genomes: GnomadNuclearOptions {
-                    enabled: query_gnomad_genomes_enabled,
-                    allele_frequency: query_gnomad_genomes_frequency,
-                    heterozygous: query_gnomad_genomes_heteroplasmic,
-                    homozygous: query_gnomad_genomes_homoplasmic,
+            frequency: QuerySettingsFrequency {
+                gnomad_genomes: GnomadNuclearFrequencySettings {
+                    enabled: query_gnomad_mtdna_enabled,
+                    frequency: query_gnomad_mtdna_frequency,
+                    heterozygous: query_gnomad_mtdna_heteroplasmic,
+                    homozygous: query_gnomad_mtdna_homoplasmic,
                     ..Default::default()
                 },
                 ..Default::default()
             },
             ..Default::default()
         };
-        let seq_var = SequenceVariant {
+        let seq_var = VariantRecord {
             population_frequencies: PopulationFrequencies {
-                gnomad: Gnomads {
-                    genomes_an: seqvar_gnomad_genomes_an,
-                    genomes_het: seqvar_gnomad_genomes_het,
-                    genomes_hom: seqvar_gnomad_genomes_hom,
+                gnomad_mt: MitochondrialFrequencies {
+                    an: seqvar_gnomad_genomes_an,
+                    het: seqvar_gnomad_genomes_het,
+                    hom: seqvar_gnomad_genomes_hom,
                     ..Default::default()
                 },
                 ..Default::default()
             },
-            chrom: "MT".to_string(),
-            reference: "G".into(),
-            alternative: "A".into(),
+            vcf_variant: VcfVariant {
+                chrom: "MT".to_string(),
+                pos: 1,
+                ref_allele: "G".into(),
+                alt_allele: "A".into(),
+            },
             ann_fields: vec![AnnField {
                 allele: mehari::annotate::seqvars::ann::Allele::Alt {
                     alternative: "A".into(),
@@ -523,6 +558,7 @@ mod test {
                 feature_type: mehari::annotate::seqvars::ann::FeatureType::SoTerm {
                     term: mehari::annotate::seqvars::ann::SoFeature::Transcript,
                 },
+                strand: Default::default(),
                 feature_id: Default::default(),
                 feature_biotype: vec![mehari::annotate::seqvars::ann::FeatureBiotype::Coding],
                 rank: Default::default(),
diff --git a/src/seqvars/query/interpreter/genes_allowlist.rs b/src/seqvars/query/interpreter/genes_allowlist.rs
index 1708aa3a..1472052f 100644
--- a/src/seqvars/query/interpreter/genes_allowlist.rs
+++ b/src/seqvars/query/interpreter/genes_allowlist.rs
@@ -1,28 +1,24 @@
 use std::collections::HashSet;
 
-use crate::seqvars::query::schema::SequenceVariant;
+use crate::seqvars::query::schema::data::VariantRecord;
 
-/// Determine whether the `SequenceVariant` passes the genes allowlist filter.
-pub fn passes(hgnc_allowlist: &Option<HashSet<String>>, seqvar: &SequenceVariant) -> bool {
-    if let Some(hgnc_allowlist) = &hgnc_allowlist {
-        if hgnc_allowlist.is_empty() {
-            true
-        } else {
-            let res = seqvar
-                .ann_fields
-                .iter()
-                .any(|ann_field| hgnc_allowlist.contains(&ann_field.gene_id));
-            if !res {
-                tracing::trace!(
-                    "variant {:?} fails gene allowlist filter {:?}",
-                    seqvar,
-                    &hgnc_allowlist
-                );
-            }
-            res
-        }
-    } else {
+/// Determine whether the `VariantRecord` passes the genes allowlist filter.
+pub fn passes(hgnc_allowlist: &HashSet<String>, seqvar: &VariantRecord) -> bool {
+    if hgnc_allowlist.is_empty() {
         true
+    } else {
+        let res = seqvar
+            .ann_fields
+            .iter()
+            .any(|ann_field| hgnc_allowlist.contains(&ann_field.gene_id));
+        if !res {
+            tracing::trace!(
+                "variant {:?} fails gene allowlist filter {:?}",
+                seqvar,
+                &hgnc_allowlist
+            );
+        }
+        res
     }
 }
 
@@ -30,48 +26,46 @@ pub fn passes(hgnc_allowlist: &Option<HashSet<String>>, seqvar: &SequenceVariant
 mod test {
     use rstest::rstest;
 
-    use crate::seqvars::query::schema::SequenceVariant;
+    use crate::seqvars::query::schema::data::VariantRecord;
     use mehari::annotate::seqvars::ann::AnnField;
 
     #[rstest]
-    #[case(None, None, true)]
+    #[case(vec![], None, true)]
     #[case(
-        Some(vec![]),
+        vec![],
         None,
         true,
     )]
     #[case(
-        Some(vec![String::from("HGNC:1100")]),
+        vec![String::from("HGNC:1100")],
         None,
         false,
     )]
     #[case(
-        Some(vec![String::from("HGNC:1")]),
+        vec![String::from("HGNC:1")],
         Some(String::from("HGNC:1100")),
         false,
     )]
     #[case(
-        Some(vec![String::from("HGNC:1100")]),
+        vec![String::from("HGNC:1100")],
         Some(String::from("HGNC:1100")),
         true,
     )]
     #[case(
-        Some(vec![String::from("HGNC:1"), String::from("HGNC:1100")]),
+        vec![String::from("HGNC:1"), String::from("HGNC:1100")],
         Some(String::from("HGNC:1100")),
         true,
     )]
     fn passes(
-        #[case] hgnc_allowlist: Option<Vec<String>>,
+        #[case] hgnc_allowlist: Vec<String>,
         #[case] seqvar_gene: Option<String>,
         #[case] expected: bool,
     ) {
-        let hgnc_allowlist = hgnc_allowlist.map(|hgnc_allowlist| {
-            hgnc_allowlist
-                .into_iter()
-                .map(|hgnc_id| hgnc_id.to_uppercase())
-                .collect::<std::collections::HashSet<_>>()
-        });
-        let seqvar = SequenceVariant {
+        let hgnc_allowlist = hgnc_allowlist
+            .into_iter()
+            .map(|hgnc_id| hgnc_id.to_uppercase())
+            .collect::<std::collections::HashSet<_>>();
+        let seqvar = VariantRecord {
             ann_fields: if let Some(gene_id) = seqvar_gene.as_ref() {
                 vec![AnnField {
                     gene_id: gene_id.clone(),
diff --git a/src/seqvars/query/interpreter/genotype.rs b/src/seqvars/query/interpreter/genotype.rs
index 8a1318fe..0da62c02 100644
--- a/src/seqvars/query/interpreter/genotype.rs
+++ b/src/seqvars/query/interpreter/genotype.rs
@@ -1,16 +1,18 @@
-use crate::seqvars::query::schema::{CaseQuery, GenotypeChoice, SequenceVariant};
+use crate::seqvars::query::schema::{
+    data::VariantRecord,
+    query::{
+        CaseQuery, GenotypeChoice, MatchesGenotypeStr as _, QuerySettingsGenotype, RecessiveMode,
+    },
+};
 
-/// Determine whether the `SequenceVariant` passes the genotype filter.
+/// Determine whether the `VariantRecord` passes the genotype filter.
 pub fn passes(
     query: &CaseQuery,
-    seqvar: &SequenceVariant,
+    seqvar: &VariantRecord,
     no_call_samples: &[&str],
 ) -> Result<bool, anyhow::Error> {
-    let result = if query.recessive_mode() {
-        let index_sample = query.index_sample().ok_or_else(|| {
-            anyhow::anyhow!("recessive mode requires an index sample, but none was found")
-        })?;
-        passes_recessive_modes(&query.genotype, &index_sample, seqvar, no_call_samples)?
+    let result = if query.genotype.recessive_mode != RecessiveMode::Disabled {
+        passes_recessive_modes(&query.genotype, seqvar, no_call_samples)?
     } else {
         passes_non_recessive_mode(&query.genotype, seqvar, no_call_samples)?
     };
@@ -27,33 +29,42 @@ pub fn passes(
 
 /// Handle case of the mode being one of the recessive modes.
 fn passes_recessive_modes(
-    query_genotype: &indexmap::IndexMap<String, Option<GenotypeChoice>>,
-    index_name: &str,
-    seqvar: &SequenceVariant,
+    query_genotype: &QuerySettingsGenotype,
+    seqvar: &VariantRecord,
     no_call_samples: &[&str],
 ) -> Result<bool, anyhow::Error> {
+    // Pick recessive index and parent names from query.
+    let index_name = query_genotype.recessive_index().map_err(|e| {
+        anyhow::anyhow!(
+            "invalid recessive index in genotype filter {:?}: {}",
+            &query_genotype,
+            e
+        )
+    })?;
+    let parent_names = query_genotype.recessive_parents().map_err(|e| {
+        anyhow::anyhow!(
+            "invalid recessive parents in genotype filter {:?}: {}",
+            &query_genotype,
+            e
+        )
+    })?;
+
     // Get genotype choice of index.
     let index_gt_choice = query_genotype
-        .get(index_name)
+        .sample_genotypes
+        .get(&index_name)
         .ok_or_else(|| {
             anyhow::anyhow!(
                 "index sample {} not found in genotype filter {:?}",
                 &index_name,
                 &query_genotype
             )
-        })?
-        .ok_or_else(|| {
-            anyhow::anyhow!(
-                "index sample {} has no genotype choice in genotype filter {:?}",
-                &index_name,
-                &query_genotype
-            )
         })?;
     // For recessive mode, we have to know the samples selected for index and parents.
-    let index_gt_string = if no_call_samples.contains(&index_name) {
+    let index_gt_string = if no_call_samples.contains(&index_name.as_str()) {
         String::from(".")
     } else {
-        let call_info = seqvar.call_info.get(index_name).ok_or_else(|| {
+        let call_info = seqvar.call_infos.get(&index_name).ok_or_else(|| {
             anyhow::anyhow!(
                 "index sample {} not found in call info for {:?}",
                 &index_name,
@@ -69,12 +80,10 @@ fn passes_recessive_modes(
         })?
     };
     let parent_names = query_genotype
+        .sample_genotypes
         .iter()
         .flat_map(|(sample, choice)| {
-            if matches!(
-                choice,
-                Some(crate::seqvars::query::schema::GenotypeChoice::RecessiveParent)
-            ) {
+            if choice.genotype == GenotypeChoice::RecessiveParent {
                 Some(sample.clone())
             } else {
                 None
@@ -88,7 +97,7 @@ fn passes_recessive_modes(
                 Ok(String::from(".")) // no-call
             } else {
                 seqvar
-                    .call_info
+                    .call_infos
                     .get(parent_name)
                     .cloned()
                     .ok_or_else(|| {
@@ -110,32 +119,18 @@ fn passes_recessive_modes(
         })
         .collect::<Result<Vec<_>, _>>()?;
 
-    let compound_recessive_ok_index = crate::seqvars::query::schema::GenotypeChoice::Het
-        .matches(&index_gt_string)
-        .map_err(|e| anyhow::anyhow!("invalid index genotype: {}", e))?;
+    let compound_recessive_ok_index = GenotypeChoice::Het.matches(&index_gt_string);
     let compound_recessive_parents_ref = parent_gt_strings
         .iter()
-        .filter(|parent_gt_string| {
-            crate::seqvars::query::schema::GenotypeChoice::Ref
-                .matches(parent_gt_string)
-                .unwrap_or(false)
-        })
+        .filter(|parent_gt_string| GenotypeChoice::Ref.matches(parent_gt_string))
         .count();
     let compound_recessive_parents_het = parent_gt_strings
         .iter()
-        .filter(|parent_gt_string| {
-            crate::seqvars::query::schema::GenotypeChoice::Het
-                .matches(parent_gt_string)
-                .unwrap_or(false)
-        })
+        .filter(|parent_gt_string| GenotypeChoice::Het.matches(parent_gt_string))
         .count();
     let compound_recessive_parents_hom = parent_gt_strings
         .iter()
-        .filter(|parent_gt_string| {
-            crate::seqvars::query::schema::GenotypeChoice::Hom
-                .matches(parent_gt_string)
-                .unwrap_or(false)
-        })
+        .filter(|parent_gt_string| GenotypeChoice::Hom.matches(parent_gt_string))
         .count();
 
     let compound_recessive_ok = match parent_names.len() {
@@ -154,25 +149,20 @@ fn passes_recessive_modes(
         _ => anyhow::bail!("more than two recessive parents selected"),
     };
 
-    let homozygous_recessive_ok_index = crate::seqvars::query::schema::GenotypeChoice::Hom
-        .matches(&index_gt_string)
-        .map_err(|e| anyhow::anyhow!("invalid index genotype: {}", e))?;
+    let homozygous_recessive_ok_index = GenotypeChoice::Hom.matches(&index_gt_string);
     let homozygous_recessive_ok_parents = parent_gt_strings
         .iter()
-        .map(|parent_gt_string| {
-            crate::seqvars::query::schema::GenotypeChoice::Het
-                .matches(parent_gt_string)
-                .map_err(|e| anyhow::anyhow!("invalid parent genotype: {}", e))
-        })
-        .collect::<Result<Vec<_>, _>>()?;
+        .map(|parent_gt_string| GenotypeChoice::Het.matches(parent_gt_string))
+        .collect::<Vec<_>>();
     let homozygous_recessive_ok =
         homozygous_recessive_ok_index && homozygous_recessive_ok_parents.iter().all(|&ok| ok);
 
-    match index_gt_choice {
-        GenotypeChoice::ComphetIndex => Ok(compound_recessive_ok),
-        GenotypeChoice::RecessiveIndex => Ok(compound_recessive_ok || homozygous_recessive_ok),
+    match query_genotype.recessive_mode {
+        RecessiveMode::CompoundHeterozygous => Ok(compound_recessive_ok),
+        RecessiveMode::Homozygous => Ok(homozygous_recessive_ok),
+        RecessiveMode::Any => Ok(compound_recessive_ok || homozygous_recessive_ok),
         _ => anyhow::bail!(
-            "invalid genotype choice for recessive mode: {:?}",
+            "invalid recessive mode choice for recessive mode: {:?}",
             index_gt_choice
         ),
     }
@@ -181,20 +171,14 @@ fn passes_recessive_modes(
 /// Handle case if the mode is not "recessive".  Note that this actually includes the
 /// homozygous recessive mode.
 fn passes_non_recessive_mode(
-    query_genotype: &indexmap::IndexMap<String, Option<GenotypeChoice>>,
-    seqvar: &SequenceVariant,
+    query_genotype: &QuerySettingsGenotype,
+    seqvar: &VariantRecord,
     no_call_samples: &[&str],
 ) -> Result<bool, anyhow::Error> {
-    for (sample_name, genotype) in query_genotype.iter() {
-        let genotype_choice = if let Some(genotype_choice) = genotype {
-            genotype_choice
-        } else {
-            tracing::trace!("no genotype choice for sample {} (skip&pass)", sample_name);
-            continue;
-        };
+    for (sample_name, genotype_choice) in query_genotype.sample_genotypes.iter() {
         let genotype = if no_call_samples.contains(&sample_name.as_str()) {
             "." // no-call
-        } else if let Some(call_info) = seqvar.call_info.get(sample_name) {
+        } else if let Some(call_info) = seqvar.call_infos.get(sample_name) {
             if let Some(genotype) = call_info.genotype.as_ref() {
                 genotype
             } else {
@@ -206,10 +190,7 @@ fn passes_non_recessive_mode(
             return Ok(false);
         };
 
-        if !genotype_choice
-            .matches(genotype)
-            .map_err(|e| anyhow::anyhow!("invalid genotype choice in {:?}: {}", &seqvar, e))?
-        {
+        if !genotype_choice.genotype.matches(genotype) {
             tracing::trace!(
                 "variant {:?} fails genotype filter {:?} on sample {}",
                 seqvar,
@@ -225,19 +206,17 @@ fn passes_non_recessive_mode(
 
 #[cfg(test)]
 mod test {
-    use rstest::rstest;
-
-    use crate::seqvars::query::schema::{
-        CallInfo,
+    use crate::seqvars::query::schema::data::{CallInfo, VariantRecord};
+    use crate::seqvars::query::schema::query::{
         GenotypeChoice::{self, *},
-        SequenceVariant,
+        QuerySettingsGenotype, RecessiveMode, SampleGenotypeChoice,
     };
 
     static INDEX_NAME: &str = "sample";
     static FATHER_NAME: &str = "father";
     static MOTHER_NAME: &str = "mother";
 
-    #[rstest]
+    #[rstest::rstest]
     // any: passes
     #[case("0/0", Any, true)]
     #[case("0|0", Any, true)]
@@ -333,20 +312,25 @@ mod test {
         #[case] query_gt: GenotypeChoice,
         #[case] expected: bool,
     ) -> Result<(), anyhow::Error> {
-        let query_genotype: indexmap::IndexMap<_, _> =
-            vec![(String::from(INDEX_NAME), Some(query_gt))]
-                .into_iter()
-                .collect();
-        let seq_var = SequenceVariant {
-            call_info: vec![(
-                INDEX_NAME.into(),
+        let query_genotype = QuerySettingsGenotype {
+            recessive_mode: RecessiveMode::Any,
+            sample_genotypes: indexmap::indexmap! {
+                String::from(INDEX_NAME) => SampleGenotypeChoice {
+                    sample: String::from(INDEX_NAME),
+                    genotype: query_gt,
+                    ..Default::default()
+                }
+            },
+        };
+
+        let seq_var = VariantRecord {
+            call_infos: indexmap::indexmap! {
+                INDEX_NAME.into() =>
                 CallInfo {
                     genotype: Some(sample_gt.into()),
                     ..Default::default()
                 },
-            )]
-            .into_iter()
-            .collect(),
+            },
             ..Default::default()
         };
 
@@ -362,7 +346,7 @@ mod test {
         Ok(())
     }
 
-    #[rstest]
+    #[rstest::rstest]
     // any: passes
     #[case("0/0,0/0,0/0", Any, Any, Any, true)]
     #[case(".,.,.", Any, Any, Any, true)]
@@ -392,43 +376,48 @@ mod test {
         #[case] query_gt_mother: GenotypeChoice,
         #[case] expected: bool,
     ) -> Result<(), anyhow::Error> {
-        let query_genotype: indexmap::IndexMap<_, _> = vec![
-            (String::from(INDEX_NAME), Some(query_gt_index)),
-            (String::from(FATHER_NAME), Some(query_gt_father)),
-            (String::from(MOTHER_NAME), Some(query_gt_mother)),
-        ]
-        .into_iter()
-        .collect();
+        let query_genotype = QuerySettingsGenotype {
+            recessive_mode: RecessiveMode::Any,
+            sample_genotypes: indexmap::indexmap! {
+                String::from(INDEX_NAME) => SampleGenotypeChoice {
+                    sample: String::from(INDEX_NAME),
+                    genotype: query_gt_index,
+                    ..Default::default()
+                },
+                String::from(FATHER_NAME) => SampleGenotypeChoice {
+                    sample: String::from(FATHER_NAME),
+                    genotype: query_gt_father,
+                    ..Default::default()
+                },
+                String::from(MOTHER_NAME) => SampleGenotypeChoice {
+                    sample: String::from(MOTHER_NAME),
+                    genotype: query_gt_mother,
+                    ..Default::default()
+                },
+            },
+        };
         let sample_gts = sample_gts
             .split(',')
             .map(|s| s.to_string())
             .collect::<Vec<_>>();
-        let seq_var = SequenceVariant {
-            call_info: vec![
-                (
-                    String::from(INDEX_NAME),
-                    CallInfo {
-                        genotype: Some(sample_gts[0].clone()),
-                        ..Default::default()
-                    },
-                ),
-                (
-                    String::from(FATHER_NAME),
-                    CallInfo {
-                        genotype: Some(sample_gts[1].clone()),
-                        ..Default::default()
-                    },
-                ),
-                (
-                    String::from(MOTHER_NAME),
-                    CallInfo {
-                        genotype: Some(sample_gts[2].clone()),
-                        ..Default::default()
-                    },
-                ),
-            ]
-            .into_iter()
-            .collect(),
+        let seq_var = VariantRecord {
+            call_infos: indexmap::indexmap! {
+                String::from(INDEX_NAME) =>
+                CallInfo {
+                    genotype: Some(sample_gts[0].clone()),
+                    ..Default::default()
+                },
+                String::from(FATHER_NAME) =>
+                CallInfo {
+                    genotype: Some(sample_gts[1].clone()),
+                    ..Default::default()
+                },
+                String::from(MOTHER_NAME) =>
+                CallInfo {
+                    genotype: Some(sample_gts[2].clone()),
+                    ..Default::default()
+                },
+            },
             ..Default::default()
         };
 
@@ -447,29 +436,32 @@ mod test {
         Ok(())
     }
 
-    #[rstest]
+    #[rstest::rstest]
     // any: passes
-    #[case("0/0", ComphetIndex)]
     #[case("0/0", RecessiveIndex)]
     #[case("0/0", RecessiveParent)]
     fn passes_non_recessive_mode_fails_on_recessive_markers(
         #[case] sample_gt: &str,
         #[case] query_gt: GenotypeChoice,
     ) -> Result<(), anyhow::Error> {
-        let query_genotype: indexmap::IndexMap<_, _> =
-            vec![(String::from(INDEX_NAME), Some(query_gt))]
-                .into_iter()
-                .collect();
-        let seq_var = SequenceVariant {
-            call_info: vec![(
-                INDEX_NAME.into(),
+        let query_genotype = QuerySettingsGenotype {
+            recessive_mode: RecessiveMode::Any,
+            sample_genotypes: indexmap::indexmap! {
+                String::from(INDEX_NAME) => SampleGenotypeChoice {
+                    sample: String::from(INDEX_NAME),
+                    genotype: query_gt,
+                    ..Default::default()
+                }
+            },
+        };
+        let seq_var = VariantRecord {
+            call_infos: indexmap::indexmap! {
+                INDEX_NAME.into() =>
                 CallInfo {
                     genotype: Some(sample_gt.into()),
                     ..Default::default()
                 },
-            )]
-            .into_iter()
-            .collect(),
+            },
             ..Default::default()
         };
 
@@ -478,22 +470,22 @@ mod test {
         Ok(())
     }
 
-    #[rstest]
-    // comphet-index: passes
-    #[case("0/1", ComphetIndex, true)]
-    #[case("0|1", ComphetIndex, true)]
-    #[case("1/0", ComphetIndex, true)]
-    #[case("1|0", ComphetIndex, true)]
-    // comphet-index: passes NOT
-    #[case("0/0", ComphetIndex, false)]
-    #[case("0|0", ComphetIndex, false)]
-    #[case("0", ComphetIndex, false)]
-    #[case("1/1", ComphetIndex, false)]
-    #[case("1|1", ComphetIndex, false)]
-    #[case("1", ComphetIndex, false)]
-    #[case(".", ComphetIndex, false)]
-    #[case("./.", ComphetIndex, false)]
-    #[case(".|.", ComphetIndex, false)]
+    #[rstest::rstest]
+    // // comphet-index: passes
+    // #[case("0/1", ComphetIndex, true)]
+    // #[case("0|1", ComphetIndex, true)]
+    // #[case("1/0", ComphetIndex, true)]
+    // #[case("1|0", ComphetIndex, true)]
+    // // comphet-index: passes NOT
+    // #[case("0/0", ComphetIndex, false)]
+    // #[case("0|0", ComphetIndex, false)]
+    // #[case("0", ComphetIndex, false)]
+    // #[case("1/1", ComphetIndex, false)]
+    // #[case("1|1", ComphetIndex, false)]
+    // #[case("1", ComphetIndex, false)]
+    // #[case(".", ComphetIndex, false)]
+    // #[case("./.", ComphetIndex, false)]
+    // #[case(".|.", ComphetIndex, false)]
     // recessive-index: passes
     #[case("0/1", RecessiveIndex, true)]
     #[case("0|1", RecessiveIndex, true)]
@@ -514,25 +506,29 @@ mod test {
         #[case] query_gt: GenotypeChoice,
         #[case] expected: bool,
     ) -> Result<(), anyhow::Error> {
-        let query_genotype: indexmap::IndexMap<_, _> =
-            vec![(String::from(INDEX_NAME), Some(query_gt))]
-                .into_iter()
-                .collect();
-        let seq_var = SequenceVariant {
-            call_info: vec![(
-                INDEX_NAME.into(),
+        let query_genotype = QuerySettingsGenotype {
+            recessive_mode: RecessiveMode::Any,
+            sample_genotypes: indexmap::indexmap! {
+                String::from(INDEX_NAME) => SampleGenotypeChoice {
+                    sample: String::from(INDEX_NAME),
+                    genotype: query_gt,
+                    ..Default::default()
+                }
+            },
+        };
+        let seq_var = VariantRecord {
+            call_infos: indexmap::indexmap! {
+                INDEX_NAME.into() =>
                 CallInfo {
                     genotype: Some(sample_gt.into()),
                     ..Default::default()
                 },
-            )]
-            .into_iter()
-            .collect(),
+            },
             ..Default::default()
         };
 
         assert_eq!(
-            super::passes_recessive_modes(&query_genotype, INDEX_NAME, &seq_var, &[])?,
+            super::passes_recessive_modes(&query_genotype, &seq_var, &[])?,
             expected,
             "sample_gt = {}, query_gt = {:?}, expected = {}",
             sample_gt,
@@ -543,7 +539,7 @@ mod test {
         Ok(())
     }
 
-    #[rstest]
+    #[rstest::rstest]
     // recessive mode: passes
     #[case("0/1,0/0,0/0", RecessiveIndex, Any, Any, true)]
     #[case("0|1,0/0,0/0", RecessiveIndex, Any, Any, true)]
@@ -561,22 +557,22 @@ mod test {
     #[case("0/1,1/1,0/0", RecessiveIndex, RecessiveParent, RecessiveParent, false)]
     #[case("0/1,0/0,1/1", RecessiveIndex, RecessiveParent, RecessiveParent, false)]
     #[case("0/1,0/1,0/1", RecessiveIndex, RecessiveParent, RecessiveParent, false)]
-    // compound recessive mode: passes
-    #[case("0/1,0/0,0/0", ComphetIndex, Any, Any, true)]
-    #[case("0|1,0/0,0/0", ComphetIndex, Any, Any, true)]
-    #[case("1/0,0/0,0/0", ComphetIndex, Any, Any, true)]
-    #[case("1|0,0/0,0/0", ComphetIndex, Any, Any, true)]
-    #[case("0/1,1/1,0/0", ComphetIndex, Any, RecessiveParent, true)]
-    #[case("0/1,0/0,1/1", ComphetIndex, RecessiveParent, Any, true)]
-    #[case("1/0,0/1,0/0", ComphetIndex, RecessiveParent, RecessiveParent, true)]
-    #[case("1/0,0/0,0/1", ComphetIndex, RecessiveParent, RecessiveParent, true)]
-    // compound recessive mode: passes NOT
-    #[case("1/1,0/1,0/1", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    #[case("1|1,0|1,1|0", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    #[case("0/1,0/0,0/0", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    #[case("0/1,1/1,0/0", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    #[case("0/1,0/0,1/1", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    #[case("0/1,0/1,0/1", ComphetIndex, RecessiveParent, RecessiveParent, false)]
+    // // compound recessive mode: passes
+    // #[case("0/1,0/0,0/0", ComphetIndex, Any, Any, true)]
+    // #[case("0|1,0/0,0/0", ComphetIndex, Any, Any, true)]
+    // #[case("1/0,0/0,0/0", ComphetIndex, Any, Any, true)]
+    // #[case("1|0,0/0,0/0", ComphetIndex, Any, Any, true)]
+    // #[case("0/1,1/1,0/0", ComphetIndex, Any, RecessiveParent, true)]
+    // #[case("0/1,0/0,1/1", ComphetIndex, RecessiveParent, Any, true)]
+    // #[case("1/0,0/1,0/0", ComphetIndex, RecessiveParent, RecessiveParent, true)]
+    // #[case("1/0,0/0,0/1", ComphetIndex, RecessiveParent, RecessiveParent, true)]
+    // // compound recessive mode: passes NOT
+    // #[case("1/1,0/1,0/1", ComphetIndex, RecessiveParent, RecessiveParent, false)]
+    // #[case("1|1,0|1,1|0", ComphetIndex, RecessiveParent, RecessiveParent, false)]
+    // #[case("0/1,0/0,0/0", ComphetIndex, RecessiveParent, RecessiveParent, false)]
+    // #[case("0/1,1/1,0/0", ComphetIndex, RecessiveParent, RecessiveParent, false)]
+    // #[case("0/1,0/0,1/1", ComphetIndex, RecessiveParent, RecessiveParent, false)]
+    // #[case("0/1,0/1,0/1", ComphetIndex, RecessiveParent, RecessiveParent, false)]
     fn passes_recessive_modes_trio(
         #[case] sample_gts: &str,
         #[case] query_gt_index: GenotypeChoice,
@@ -584,48 +580,53 @@ mod test {
         #[case] query_gt_mother: GenotypeChoice,
         #[case] expected: bool,
     ) -> Result<(), anyhow::Error> {
-        let query_genotype: indexmap::IndexMap<_, _> = vec![
-            (String::from(INDEX_NAME), Some(query_gt_index)),
-            (String::from(FATHER_NAME), Some(query_gt_father)),
-            (String::from(MOTHER_NAME), Some(query_gt_mother)),
-        ]
-        .into_iter()
-        .collect();
+        let query_genotype = QuerySettingsGenotype {
+            recessive_mode: RecessiveMode::Any,
+            sample_genotypes: indexmap::indexmap! {
+                String::from(INDEX_NAME) => SampleGenotypeChoice {
+                    sample: String::from(INDEX_NAME),
+                    genotype: query_gt_index,
+                    ..Default::default()
+                },
+                String::from(FATHER_NAME) => SampleGenotypeChoice {
+                    sample: String::from(FATHER_NAME),
+                    genotype: query_gt_father,
+                    ..Default::default()
+                },
+                String::from(MOTHER_NAME) => SampleGenotypeChoice {
+                    sample: String::from(MOTHER_NAME),
+                    genotype: query_gt_mother,
+                    ..Default::default()
+                },
+            },
+        };
         let sample_gts = sample_gts
             .split(',')
             .map(|s| s.to_string())
             .collect::<Vec<_>>();
-        let seq_var = SequenceVariant {
-            call_info: vec![
-                (
-                    String::from(INDEX_NAME),
-                    CallInfo {
-                        genotype: Some(sample_gts[0].clone()),
-                        ..Default::default()
-                    },
-                ),
-                (
-                    String::from(FATHER_NAME),
-                    CallInfo {
-                        genotype: Some(sample_gts[1].clone()),
-                        ..Default::default()
-                    },
-                ),
-                (
-                    String::from(MOTHER_NAME),
-                    CallInfo {
-                        genotype: Some(sample_gts[2].clone()),
-                        ..Default::default()
-                    },
-                ),
-            ]
-            .into_iter()
-            .collect(),
+        let seq_var = VariantRecord {
+            call_infos: indexmap::indexmap! {
+                String::from(INDEX_NAME) =>
+                CallInfo {
+                    genotype: Some(sample_gts[0].clone()),
+                    ..Default::default()
+                },
+                String::from(FATHER_NAME) =>
+                CallInfo {
+                    genotype: Some(sample_gts[1].clone()),
+                    ..Default::default()
+                },
+                String::from(MOTHER_NAME) =>
+                CallInfo {
+                    genotype: Some(sample_gts[2].clone()),
+                    ..Default::default()
+                },
+            },
             ..Default::default()
         };
 
         assert_eq!(
-            super::passes_recessive_modes(&query_genotype, INDEX_NAME, &seq_var, &[])?,
+            super::passes_recessive_modes(&query_genotype, &seq_var, &[])?,
             expected,
             "sample_gt = {:?}, query_gt_index = {:?}, query_gt_father = {:?}, \
             query_gt_mother = {:?}, expected = {}",
diff --git a/src/seqvars/query/interpreter/mod.rs b/src/seqvars/query/interpreter/mod.rs
index e2689a04..8ea2a9a7 100644
--- a/src/seqvars/query/interpreter/mod.rs
+++ b/src/seqvars/query/interpreter/mod.rs
@@ -1,4 +1,4 @@
-//! Apply settings from a `strucvar::query::schema::CaseQuery` to `SequenceVariant` records.
+//! Apply settings from a `strucvar::query::schema::CaseQuery` to `VariantRecord` records.
 
 use std::collections::HashSet;
 
@@ -12,7 +12,7 @@ mod regions_allowlist;
 
 use super::{
     annonars::Annotator,
-    schema::{CaseQuery, SequenceVariant},
+    schema::{data::VariantRecord, query::CaseQuery},
 };
 
 /// Hold data structures that support the interpretation of one `CaseQuery`
@@ -22,7 +22,7 @@ pub struct QueryInterpreter {
     /// The case query settings.
     pub query: CaseQuery,
     /// Gene allowlist with HGNC IDs.
-    pub hgnc_allowlist: Option<HashSet<String>>,
+    pub hgnc_allowlist: HashSet<String>,
 }
 
 /// Result type for `QueryInterpreter::passes_genotype()`.
@@ -34,17 +34,17 @@ pub struct PassesResult {
 
 impl QueryInterpreter {
     /// Construct new `QueryInterpreter` with the given query settings.
-    pub fn new(query: CaseQuery, hgnc_allowlist: Option<HashSet<String>>) -> Self {
+    pub fn new(query: CaseQuery, hgnc_allowlist: HashSet<String>) -> Self {
         QueryInterpreter {
             query,
             hgnc_allowlist,
         }
     }
 
-    /// Determine whether the annotated `SequenceVariant` passes all criteria.
+    /// Determine whether the annotated `VariantRecord` passes all criteria.
     pub fn passes(
         &self,
-        seqvar: &SequenceVariant,
+        seqvar: &VariantRecord,
         annotator: &Annotator,
     ) -> Result<PassesResult, anyhow::Error> {
         // Check the filters first that are cheap to compute.
diff --git a/src/seqvars/query/interpreter/quality.rs b/src/seqvars/query/interpreter/quality.rs
index 93a26c2e..196938ac 100644
--- a/src/seqvars/query/interpreter/quality.rs
+++ b/src/seqvars/query/interpreter/quality.rs
@@ -1,7 +1,8 @@
 use crate::{
     common::strip_gt_leading_slash,
     seqvars::query::schema::{
-        CallInfo, CaseQuery, FailFilterChoice, SampleQualitySettings, SequenceVariant,
+        data::{CallInfo, VariantRecord},
+        query::{CaseQuery, SampleQualitySettings},
     },
 };
 
@@ -14,31 +15,26 @@ pub struct PassOrNoCall {
     pub no_call_samples: Vec<String>,
 }
 
-/// Determine whether the `SequenceVariant` passes the quality filter.
+/// Determine whether the `VariantRecord` passes the quality filter.
 /// Will return `FailFilterChoice::Ignore` if the variant passes.
-pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result<PassOrNoCall, anyhow::Error> {
+pub fn passes(query: &CaseQuery, seqvar: &VariantRecord) -> Result<PassOrNoCall, anyhow::Error> {
     let mut result = PassOrNoCall {
         pass: true,
         no_call_samples: Vec::new(),
     };
-    for (sample_name, quality_settings) in &query.quality {
-        if let Some(call_info) = seqvar.call_info.get(sample_name) {
-            if let Some(fail) = passes_for_sample(quality_settings, call_info) {
-                match fail {
-                    FailFilterChoice::Ignore => {
-                        // ignore quality failure for sample
-                    }
-                    FailFilterChoice::Drop => {
-                        tracing::trace!(
-                            "sample {} (call_info={:?}) in variant {:?} fails quality filter {:?}",
-                            &sample_name,
-                            &call_info,
-                            &seqvar,
-                            &quality_settings
-                        );
-                        result.pass = false;
-                        break;
-                    }
+    for (sample_name, quality_settings) in &query.quality.sample_qualities {
+        if let Some(call_info) = seqvar.call_infos.get(sample_name) {
+            if !passes_for_sample(quality_settings, call_info) {
+                tracing::trace!(
+                    "sample {} (call_info={:?}) in variant {:?} fails quality filter {:?}",
+                    &sample_name,
+                    &call_info,
+                    &seqvar,
+                    &quality_settings
+                );
+                if quality_settings.filter_active {
+                    result.pass = false;
+                    break;
                 }
             } else {
                 // no failure, all good
@@ -57,11 +53,9 @@ pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result<PassOrNoCal
     Ok(result)
 }
 
-/// Return failure code (or None for all-pass) for one sample's call info.
-fn passes_for_sample(
-    quality_settings: &SampleQualitySettings,
-    call_info: &CallInfo,
-) -> Option<FailFilterChoice> {
+/// Return whether the sample passes the quality filter.
+fn passes_for_sample(quality_settings: &SampleQualitySettings, call_info: &CallInfo) -> bool {
+    // Ad-hoc enum for genotype.
     #[derive(PartialEq, Eq)]
     enum Genotype {
         Het,
@@ -82,116 +76,105 @@ fn passes_for_sample(
         Genotype::NoCall
     };
 
-    // dp_het/dp_hom and ab
+    // min_dp_het, min_dp_hom, and min_ab
     match genotype {
         Genotype::Het => {
-            // dp_het
-            if let Some(dp_het) = quality_settings.dp_het {
-                if let Some(dp) = call_info.dp {
-                    if dp < dp_het {
-                        return Some(quality_settings.filter_active);
-                    }
+            // min_dp_het
+            if let (Some(min_dp_het), Some(dp)) = (quality_settings.min_dp_het, call_info.dp) {
+                if dp < min_dp_het {
+                    return false;
                 }
             }
 
-            // ab
-            if let (Some(settings_ab), Some(call_dp), Some(call_ad)) =
-                (quality_settings.ab, call_info.dp, call_info.ad)
+            // min_ab
+            if let (Some(min_ab), Some(call_dp), Some(call_ad)) =
+                (quality_settings.min_ab, call_info.dp, call_info.ad)
             {
                 let ab_raw = call_ad as f64 / call_dp as f64;
                 let ab = if ab_raw > 0.5 { 1.0 - ab_raw } else { ab_raw };
                 let eps = 1e-6f64;
-                if ab + eps < settings_ab as f64 {
-                    return Some(quality_settings.filter_active);
+                if ab + eps < min_ab as f64 {
+                    return false;
                 }
             }
         }
         Genotype::Hom => {
-            if let Some(dp_hom) = quality_settings.dp_hom {
-                if let Some(dp) = call_info.dp {
-                    if dp < dp_hom {
-                        return Some(quality_settings.filter_active);
-                    }
+            // min_dp_hom
+            if let (Some(dp_hom), Some(dp)) = (quality_settings.min_dp_hom, call_info.dp) {
+                if dp < dp_hom {
+                    return false;
                 }
             }
         }
         Genotype::Ref | Genotype::NoCall => (),
     }
 
-    // gq
-    if let (Some(settings_gq), Some(call_gq)) = (quality_settings.gq, call_info.quality) {
+    // min_gq
+    if let (Some(settings_gq), Some(call_gq)) = (quality_settings.min_gq, call_info.quality) {
         if call_gq < settings_gq as f32 {
-            return Some(quality_settings.filter_active);
+            return false;
         }
     }
 
     if genotype != Genotype::Ref {
-        // ad
-        if let (Some(settings_ad), Some(call_ad)) = (quality_settings.ad, call_info.ad) {
+        // min_ad
+        if let (Some(settings_ad), Some(call_ad)) = (quality_settings.min_ad, call_info.ad) {
             if call_ad < settings_ad {
-                return Some(quality_settings.filter_active);
+                return false;
             }
         }
 
-        // ad_max
-        if let (Some(settings_ad_max), Some(call_ad)) = (quality_settings.ad_max, call_info.ad) {
+        // max_ad
+        if let (Some(settings_ad_max), Some(call_ad)) = (quality_settings.max_ad, call_info.ad) {
             if call_ad > settings_ad_max {
-                return Some(quality_settings.filter_active);
+                return false;
             }
         }
     }
 
-    None
+    true
 }
 
 #[cfg(test)]
 mod test {
-    use rstest::rstest;
-
-    use crate::seqvars::query::schema::{
-        CallInfo, CaseQuery,
-        FailFilterChoice::{self, *},
-        SampleQualitySettings, SequenceVariant,
+    use crate::seqvars::query::schema::data::{CallInfo, VariantRecord};
+    use crate::seqvars::query::schema::query::{
+        CaseQuery, QuerySettingsQuality, SampleQualitySettings,
     };
 
-    #[rstest]
-    #[case(Ignore, true, true, false)]
-    #[case(Ignore, false, true, false)]
-    #[case(Drop, true, true, false)]
-    #[case(Drop, false, false, false)]
+    #[rstest::rstest]
+    #[case(false, true, true, false)]
+    #[case(false, false, true, false)]
+    #[case(true, true, true, false)]
+    #[case(true, false, false, false)]
     fn passes(
-        #[case] q_fail: FailFilterChoice,
+        #[case] filter_active: bool,
         #[case] should_pass: bool,
         #[case] expected_pass: bool,
         #[case] any_no_call_sample: bool,
     ) -> Result<(), anyhow::Error> {
         let query = CaseQuery {
-            quality: vec![(
-                String::from("sample"),
-                SampleQualitySettings {
-                    filter_active: q_fail,
-                    dp_het: None,
-                    dp_hom: None,
-                    gq: if should_pass { None } else { Some(40) },
-                    ab: None,
-                    ad: None,
-                    ad_max: None,
+            quality: QuerySettingsQuality {
+                sample_qualities: indexmap::indexmap! {
+                    String::from("sample") =>
+                    SampleQualitySettings {
+                        sample: String::from("sample"),
+                        filter_active,
+                        min_gq: if should_pass { None } else { Some(40) },
+                        ..Default::default()
+                    },
                 },
-            )]
-            .into_iter()
-            .collect(),
+            },
             ..Default::default()
         };
-        let seqvar = SequenceVariant {
-            call_info: vec![(
-                String::from("sample"),
+        let seqvar = VariantRecord {
+            call_infos: indexmap::indexmap! {
+                String::from("sample") =>
                 CallInfo {
                     quality: if should_pass { None } else { Some(30f32) },
                     ..Default::default()
                 },
-            )]
-            .into_iter()
-            .collect(),
+            },
             ..Default::default()
         };
 
@@ -216,272 +199,274 @@ mod test {
         Ok(())
     }
 
-    #[rstest]
+    #[rstest::rstest]
     #[allow(clippy::too_many_arguments)]
     // het, pass dp
     #[case(
-        Some(10), // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        None, // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        Some(10), // q_min_dp_het
+        None, // q_dpmin__hom
+        None, // q_min_gq
+        None, // q_min_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         Some("0/1"), // c_genotype
         None, // c_quality
         Some(10), // c_dp
         None, // c_ad
-        None,  // expected, None = pass
+        true, // expected
     )]
     // het, fail dp
     #[case(
-        Some(10), // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        None, // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        Some(10), // q_min_dp_het
+        None, // q_dpmin__hom
+        None, // q_min_gq
+        None, // q_min_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         Some("0/1"), // c_genotype
         None, // c_quality
         Some(9), // c_dp
         None, // c_ad
-        Some(Ignore),  // expected, None = pass
+        true,  // expected
     )]
     // hom, pass dp
     #[case(
-        None, // q_dp_het
-        Some(10), // q_dp_hom
-        None, // q_gq
-        None, // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        Some(10), // q_min_dp_hom
+        None, // q_min_gq
+        None, // q_min_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         Some("1/1"), // c_genotype
         None, // c_quality
         Some(10), // c_dp
         None, // c_ad
-        None,  // expected, None = pass
+        true, // expected
     )]
     // hom, fail dp
     #[case(
-        None, // q_dp_het
-        Some(10), // q_dp_hom
-        None, // q_gq
-        None, // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        Some(10), // q_min_dp_hom
+        None, // q_min_gq
+        None, // q_min_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         Some("1/1"), // c_genotype
         None, // c_quality
         Some(9), // c_dp
         None, // c_ad
-        Some(Ignore),  // expected, None = pass
+        true,  // expected
     )]
     // pass gq
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        Some(10), // q_gq
-        None, // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        Some(10), // min_q_gq
+        None, // q_min_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         None, // c_genotype
         Some(10f32), // c_quality
         None, // c_dp
         None, // c_ad
-        None,  // expected, None = pass
+        true, // expected
     )]
     // fail gq
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        Some(10), // q_gq
-        None, // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        Some(10), // min_q_gq
+        None, // q_min_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         Some("0/1"), // c_genotype
         Some(9f32), // c_quality
         None, // c_dp
         None, // c_ad
-        Some(Ignore),  // expected, None = pass
+        true,  // expected
     )]
     // het, pass ab lower
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        Some(0.2), // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        None, // q_min_gq
+        Some(0.2), //min_ q_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         Some("0/1"), // c_genotype
         None, // c_quality
         Some(100), // c_dp
         Some(20), // c_ad
-        None,  // expected, None = pass
+        true, // expected
     )]
     // het, pass ab upper
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        Some(0.2), // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        None, // q_min_gq
+        Some(0.2), //min_ q_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         Some("0/1"), // c_genotype
         None, // c_quality
         Some(100), // c_dp
         Some(80), // c_ad
-        None,  // expected, None = pass
+        true, // expected
     )]
     // het, fail ab lower
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        Some(0.2), // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        None, // q_min_gq
+        Some(0.2), //min_ q_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         Some("0/1"), // c_genotype
         None, // c_quality
         Some(100), // c_dp
         Some(19), // c_ad
-        Some(Ignore),  // expected, None = pass
+        true,  // expected
     )]
     // het, fail ab upper
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        Some(0.2), // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        None, // q_min_gq
+        Some(0.2), //min_ q_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         Some("0/1"), // c_genotype
         None, // c_quality
         Some(100), // c_dp
         Some(81), // c_ad
-        Some(Ignore),  // expected, None = pass
+        true,  // expected
     )]
     // hom, ab ignored
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        Some(0.2), // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        None, // q_min_gq
+        Some(0.2), //min_ q_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         Some("1/1"), // c_genotype
         None, // c_quality
         None, // c_dp
         None, // c_ad
-        None,  // expected, None = pass
+        true, // expected
     )]
     // pass ad
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        None, // q_ab
-        Some(10), // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        None, // q_min_gq
+        None, // q_min_ab
+        Some(10), // min_q_ad
+        None, // q_max_ad
+        false, // filter_active
         None, // c_genotype
         None, // c_quality
         None, // c_dp
         Some(10), // c_ad
-        None,  // expected, None = pass
+        true, // expected
     )]
     // fail ad
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        None, // q_ab
-        Some(10), // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        None, // q_min_gq
+        None, // q_min_ab
+        Some(10), // min_q_ad
+        None, // q_max_ad
+        false, // filter_active
         None, // c_genotype
         None, // c_quality
         None, // c_dp
         Some(9), // c_ad
-        Some(Ignore),  // expected, None = pass
+        true,  // expected
     )]
     // pass ad_max
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        None, // q_ab
-        None, // q_ad
-        Some(10), // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        None, // q_min_gq
+        None, // q_min_ab
+        None, // q_min_ad
+        Some(10), // max_ad
+        false, // filter_active
         None, // c_genotype
         None, // c_quality
         None, // c_dp
         Some(10), // c_ad
-        None,  // expected, None = pass
+        true, // expected
     )]
     // fail ad_max
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        None, // q_ab
-        None, // q_ad
-        Some(10), // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        None, // q_min_gq
+        None, // q_min_ab
+        None, // q_min_ad
+        Some(10), // max_ad
+        false, // filter_active
         None, // c_genotype
         None, // c_quality
         None, // c_dp
         Some(11), // c_ad
-        Some(Ignore),  // expected, None = pass
+        true,  // expected
     )]
     // all none
     #[case(
-        None, // q_dp_het
-        None, // q_dp_hom
-        None, // q_gq
-        None, // q_ab
-        None, // q_ad
-        None, // q_ad_max
-        Ignore, // q_fail
+        None, // q_min_dp_het
+        None, // q_min_dp_hom
+        None, // q_min_gq
+        None, // q_min_ab
+        None, // q_min_ad
+        None, // q_max_ad
+        false, // filter_active
         None, // c_genotype
         None, // c_quality
         None, // c_dp
         None, // c_ad
-        None,  // expected, None = pass
+        true, // expected
     )]
     fn passes_for_sample(
-        #[case] q_dp_het: Option<i32>,
-        #[case] q_dp_hom: Option<i32>,
-        #[case] q_gq: Option<i32>,
-        #[case] q_ab: Option<f32>,
-        #[case] q_ad: Option<i32>,
-        #[case] q_ad_max: Option<i32>,
-        #[case] q_fail: FailFilterChoice,
+        #[case] q_min_dp_het: Option<i32>,
+        #[case] q_min_dp_hom: Option<i32>,
+        #[case] q_min_gq: Option<i32>,
+        #[case] q_min_ab: Option<f32>,
+        #[case] q_min_ad: Option<i32>,
+        #[case] q_max_ad: Option<i32>,
+        #[case] filter_active: bool,
         #[case] c_genotype: Option<&'static str>,
         #[case] c_quality: Option<f32>,
         #[case] c_dp: Option<i32>,
         #[case] c_ad: Option<i32>,
-        #[case] expected: Option<FailFilterChoice>,
+        #[case] expected: bool,
     ) -> Result<(), anyhow::Error> {
         let settings = SampleQualitySettings {
-            filter_active: q_fail,
-            dp_het: q_dp_het,
-            dp_hom: q_dp_hom,
-            gq: q_gq,
-            ab: q_ab,
-            ad: q_ad,
-            ad_max: q_ad_max,
+            sample: String::from("sample"),
+            filter_active,
+            min_dp_het: q_min_dp_het,
+            min_dp_hom: q_min_dp_hom,
+            min_gq: q_min_gq,
+            min_ab: q_min_ab,
+            min_ad: q_min_ad,
+            max_ad: q_max_ad,
         };
         let call_info = CallInfo {
+            sample: String::from("sample"),
             genotype: c_genotype.map(|s| s.to_string()),
             quality: c_quality,
             dp: c_dp,
diff --git a/src/seqvars/query/interpreter/regions_allowlist.rs b/src/seqvars/query/interpreter/regions_allowlist.rs
index 9fff9378..e6ecdb15 100644
--- a/src/seqvars/query/interpreter/regions_allowlist.rs
+++ b/src/seqvars/query/interpreter/regions_allowlist.rs
@@ -1,30 +1,27 @@
-use crate::seqvars::query::schema::{CaseQuery, GenomicRegion, Range, SequenceVariant};
+use crate::seqvars::query::schema::data::VariantRecord;
+use crate::seqvars::query::schema::query::{CaseQuery, GenomicRegion, Range};
 
-/// Determine whether the `SequenceVariant` passes the regions allowlist filter.
-pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> bool {
-    if let Some(region_allowlist) = &query.locus.genomic_regions {
-        if region_allowlist.is_empty() {
-            true
-        } else {
-            let res = region_allowlist.iter().any(|region| {
-                overlaps(
-                    region,
-                    &seqvar.chrom,
-                    seqvar.pos,
-                    seqvar.pos + seqvar.reference.len() as i32 - 1,
-                )
-            });
-            if !res {
-                tracing::trace!(
-                    "variant {:?} fails region allowlist filter {:?}",
-                    seqvar,
-                    &region_allowlist
-                );
-            }
-            res
-        }
-    } else {
+/// Determine whether the `VariantRecord` passes the regions allowlist filter.
+pub fn passes(query: &CaseQuery, seqvar: &VariantRecord) -> bool {
+    if query.locus.genome_regions.is_empty() {
         true
+    } else {
+        let res = query.locus.genome_regions.iter().any(|region| {
+            overlaps(
+                region,
+                &seqvar.vcf_variant.chrom,
+                seqvar.vcf_variant.pos,
+                seqvar.vcf_variant.pos + seqvar.vcf_variant.ref_allele.len() as i32 - 1,
+            )
+        });
+        if !res {
+            tracing::trace!(
+                "variant {:?} fails region allowlist filter {:?}",
+                seqvar,
+                &query.locus.genome_regions
+            );
+        }
+        res
     }
 }
 
diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs
index 26442990..ff07d96e 100644
--- a/src/seqvars/query/mod.rs
+++ b/src/seqvars/query/mod.rs
@@ -12,22 +12,21 @@ use std::time::Instant;
 use clap::{command, Parser};
 use ext_sort::LimitedBufferBuilder;
 use ext_sort::{ExternalSorter, ExternalSorterBuilder};
-use itertools::Itertools;
 
+use itertools::Itertools as _;
 use mehari::annotate::seqvars::CHROM_TO_CHROM_NO;
 use noodles::vcf;
 use rand_core::{RngCore, SeedableRng};
+use schema::data::{TryFromVcf as _, VariantRecord, VcfVariant};
+use schema::query::{CaseQuery, GenotypeChoice, RecessiveMode, SampleGenotypeChoice};
 use thousands::Separable;
 use uuid::Uuid;
 
 use crate::common;
-use crate::seqvars::query::schema::GenotypeChoice;
 use crate::{common::trace_rss_now, common::GenomeRelease};
 use mehari::common::noodles::open_vcf_reader;
 
 use self::annonars::Annotator;
-use self::schema::CaseQuery;
-use self::schema::SequenceVariant;
 use self::sorting::{ByCoordinate, ByHgncId};
 
 /// Command line arguments for `seqvars query` sub command.
@@ -77,55 +76,46 @@ struct QueryStats {
 
 /// Checks whether the variants pass through the query interpreter.
 ///
-/// This function is only relevant if the query uses recessive mode.
-fn passes_for_gene(
-    query: &CaseQuery,
-    seqvars: &Vec<SequenceVariant>,
-) -> Result<bool, anyhow::Error> {
-    #[derive(Debug, Clone, PartialEq, Eq)]
-    enum Mode {
-        ComphetRecessive,
-        Recessive,
-        Other,
+/// This function is only relevant if the query uses comp. het. or "any" recessive mode.
+///
+/// The case of homozygous recessive mode is assumed to be handled outside.  This function
+/// only gets passed variants that are het. in the index.
+fn passes_for_gene(query: &CaseQuery, seqvars: &Vec<VariantRecord>) -> Result<bool, anyhow::Error> {
+    // Short-circuit in case of disabled or homozygous-only recessive mode.
+    if matches!(
+        query.genotype.recessive_mode,
+        RecessiveMode::Disabled | RecessiveMode::Homozygous
+    ) {
+        return Ok(true);
     }
 
-    let mut mode = Mode::Other;
-    let mut index_name = String::default();
-    let mut parents = Vec::new();
-    query
-        .genotype
-        .iter()
-        .for_each(|(sample_name, genotype_choice)| match genotype_choice {
-            Some(GenotypeChoice::ComphetIndex) => {
-                index_name.clone_from(sample_name);
-                mode = Mode::ComphetRecessive;
-            }
-            Some(GenotypeChoice::RecessiveIndex) => {
-                index_name.clone_from(sample_name);
-                mode = Mode::Recessive;
-            }
-            Some(GenotypeChoice::RecessiveParent) => {
-                parents.push(sample_name.clone());
+    // Extract family information for recessive mode.
+    let (index, parents) = {
+        let mut index = String::new();
+        let mut parents = Vec::new();
+        for (sample_name, SampleGenotypeChoice { genotype, .. }) in
+            query.genotype.sample_genotypes.iter()
+        {
+            match genotype {
+                GenotypeChoice::RecessiveIndex => {
+                    index = sample_name.clone();
+                }
+                GenotypeChoice::RecessiveParent => {
+                    parents.push(sample_name.clone());
+                }
+                _ => (),
             }
-            _ => (),
-        });
-
-    eprintln!(
-        "mode = {:?}, index_name = {:?}, parents = {:?}",
-        mode, &index_name, &parents
-    );
-
-    // No special handling for non-recessive mode.
-    if mode == Mode::Other {
-        return Ok(true);
-    }
+        }
+        (index, parents)
+    };
+    tracing::debug!("index = {}, parents ={:?}", &index, &parents);
 
     let mut seen_het_parents = Vec::new();
     for seqvar in seqvars {
         // Get parsed index genotype.
         let index_gt: common::Genotype = seqvar
-            .call_info
-            .get(&index_name)
+            .call_infos
+            .get(&index)
             .expect("no call info for index")
             .genotype
             .as_ref()
@@ -133,16 +123,12 @@ fn passes_for_gene(
             .parse()
             .map_err(|e| anyhow::anyhow!("could not parse index genotype: {}", e))?;
 
-        eprintln!(
-            "seqvar = {:?}, index_gt = {:?}, mode = {:?}",
-            &seqvar, &index_gt, mode
-        );
-        if mode == Mode::Recessive && index_gt == common::Genotype::HomAlt {
-            // if hom. recessive is allowed then we are done
-            return Ok(true);
-        } else if mode != Mode::Recessive && index_gt != common::Genotype::Het {
-            // it only makese sense to continue in recessive mode if the index is het.
-            return Ok(false);
+        tracing::debug!("seqvar = {:?}, index_gt = {:?}", &seqvar, &index_gt);
+
+        // Index is not het., don't consider variant further for comp. het.
+        if index_gt != common::Genotype::Het {
+            // Skip variant,
+            continue;
         }
 
         // Otherwise, the index must be Het and we have to check which parent is also het.
@@ -151,7 +137,7 @@ fn passes_for_gene(
             .iter()
             .map(|parent_name| {
                 seqvar
-                    .call_info
+                    .call_infos
                     .get(parent_name)
                     .expect("no call info for parent")
                     .genotype
@@ -160,21 +146,37 @@ fn passes_for_gene(
                     .parse::<common::Genotype>()
             })
             .collect::<Result<Vec<_>, _>>()?;
+        let homalt_parents = parents
+            .iter()
+            .zip(parent_gts.iter())
+            .filter(|(_, gt)| **gt == common::Genotype::HomAlt)
+            .map(|(name, _)| name.clone())
+            .collect::<Vec<_>>();
         let het_parents = parents
             .iter()
             .zip(parent_gts.iter())
             .filter(|(_, gt)| **gt == common::Genotype::Het)
             .map(|(name, _)| name.clone())
             .collect::<Vec<_>>();
-        assert!(het_parents.len() <= 1);
-        eprintln!("het_parents = {:?}", &het_parents);
+
+        if !homalt_parents.is_empty() {
+            // Skip variants, found homozygous parent.
+            continue;
+        }
+        if het_parents.len() > 1 {
+            // Skip variants, found more than one het. parent.
+            continue;
+        }
+
+        tracing::debug!("het_parents = {:?}", &het_parents);
+
         if let Some(parent) = het_parents.first() {
             if !seen_het_parents.contains(parent) {
                 seen_het_parents.push(parent.clone());
             }
         }
 
-        eprintln!("seen_het_parents = {:?}", &seen_het_parents);
+        tracing::debug!("seen_het_parents = {:?}", &seen_het_parents);
 
         // If the number of seen het. parents is equal to the number of parents, we are done.
         if seen_het_parents.len() == parents.len() {
@@ -182,7 +184,7 @@ fn passes_for_gene(
         }
     }
 
-    // one of the recessive modes was active and we did not find all parents
+    // We did not find a compound heterozygous variant.
     Ok(false)
 }
 
@@ -233,7 +235,7 @@ async fn run_query(
             }
 
             stats.count_total += 1;
-            let record_seqvar = SequenceVariant::from_vcf(&record_buf, &input_header)
+            let record_seqvar = VariantRecord::try_from_vcf(&record_buf, &input_header)
                 .map_err(|e| anyhow::anyhow!("could not parse VCF record: {}", e))?;
             tracing::debug!("processing record {:?}", record_seqvar);
 
@@ -294,7 +296,7 @@ async fn run_query(
 
         sorted_iter
             .map(|res| res.expect("problem reading line after sorting by HGNC ID"))
-            .group_by(|by_hgnc_id| by_hgnc_id.hgnc_id.clone())
+            .chunk_by(|by_hgnc_id| by_hgnc_id.hgnc_id.clone())
             .into_iter()
             .map(|(_, group)| {
                 group
@@ -382,7 +384,7 @@ async fn run_query(
         } else {
             anyhow::bail!("error reading line from input file")
         };
-        let seqvar: SequenceVariant = serde_json::from_str(&line).map_err(|e| {
+        let seqvar: VariantRecord = serde_json::from_str(&line).map_err(|e| {
             anyhow::anyhow!(
                 "error parsing line from input file: {:?} (line: {:?})",
                 e,
@@ -406,9 +408,9 @@ async fn run_query(
 
 /// Create output payload and write the record to the output file.
 fn create_payload_and_write_record(
-    seqvar: SequenceVariant,
+    seqvar: VariantRecord,
     annotator: &Annotator,
-    chrom_to_chrom_no: &CHROM_TO_CHROM_NO,
+    chrom_to_chrom_no: &std::collections::HashMap<String, u32>,
     csv_writer: &mut csv::Writer<std::fs::File>,
     args: &Args,
     rng: &mut rand::rngs::StdRng,
@@ -430,16 +432,15 @@ fn create_payload_and_write_record(
         )
         .build()
         .map_err(|e| anyhow::anyhow!("could not build payload: {}", e))?;
-    eprintln!("result_payload = {:?}", &result_payload);
-    let start = seqvar.pos;
-    let end = start + seqvar.reference.len() as i32 - 1;
+    tracing::debug!("result_payload = {:?}", &result_payload);
+    let VcfVariant {
+        chrom,
+        pos: start,
+        ref_allele,
+        alt_allele,
+    } = seqvar.vcf_variant.clone();
+    let end = start + ref_allele.len() as i32 - 1;
     let bin = mehari::annotate::seqvars::binning::bin_from_range(start - 1, end)? as u32;
-    let SequenceVariant {
-        chrom: chromosome,
-        reference,
-        alternative,
-        ..
-    } = seqvar;
     csv_writer
         .serialize(
             &output::RecordBuilder::default()
@@ -452,17 +453,13 @@ fn create_payload_and_write_record(
                     GenomeRelease::Grch37 => "GRCh37".into(),
                     GenomeRelease::Grch38 => "GRCh38".into(),
                 })
-                .chromosome_no(
-                    *chrom_to_chrom_no
-                        .get(&chromosome)
-                        .expect("invalid chromosome") as i32,
-                )
-                .chromosome(chromosome)
+                .chromosome_no(*chrom_to_chrom_no.get(&chrom).expect("invalid chromosome") as i32)
+                .chromosome(chrom)
                 .start(start)
                 .end(end)
                 .bin(bin)
-                .reference(reference)
-                .alternative(alternative)
+                .reference(ref_allele)
+                .alternative(alt_allele)
                 .payload(
                     serde_json::to_string(&result_payload)
                         .map_err(|e| anyhow::anyhow!("could not serialize payload: {}", e))?,
@@ -489,13 +486,13 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
     };
 
     tracing::info!("Loading query... {}", args.path_query_json);
-    let query: schema::CaseQuery =
+    let query: CaseQuery =
         match serde_json::from_reader(std::fs::File::open(&args.path_query_json)?) {
             Ok(query) => query,
             Err(_) => {
-                let query: crate::pbs::seqvars::CaseQuery =
+                let query: crate::pbs::varfish::v1::seqvars::query::CaseQuery =
                     serde_json::from_reader(std::fs::File::open(&args.path_query_json)?)?;
-                CaseQuery::from(query)
+                CaseQuery::try_from(query)?
             }
         };
 
@@ -528,18 +525,8 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
     trace_rss_now();
 
     tracing::info!("Translating gene allow list...");
-    let hgnc_allowlist = if let Some(gene_allowlist) = &query.locus.gene_allowlist {
-        if gene_allowlist.is_empty() {
-            None
-        } else {
-            Some(crate::strucvars::query::translate_gene_allowlist(
-                gene_allowlist,
-                &in_memory_dbs,
-            ))
-        }
-    } else {
-        None
-    };
+    let hgnc_allowlist =
+        crate::strucvars::query::translate_genes(&query.locus.genes, &in_memory_dbs);
 
     tracing::info!("Running queries...");
     let before_query = Instant::now();
@@ -574,85 +561,81 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
 mod test {
     use rstest::rstest;
 
-    use super::schema::{CallInfo, SequenceVariant};
-    use crate::seqvars::query::schema::{CaseQuery, GenotypeChoice};
+    use super::schema::data::{CallInfo, VariantRecord};
+    use crate::seqvars::query::schema::query::{CaseQuery, GenotypeChoice, RecessiveMode};
 
     #[rstest]
     #[case(
-        GenotypeChoice::ComphetIndex,
+        RecessiveMode::CompoundHeterozygous,
         vec!["0/1,0/1,0/0"],
         false,
     )]
     #[case(
-        GenotypeChoice::ComphetIndex,
+        RecessiveMode::CompoundHeterozygous,
         vec!["1/1,0/0,0/0"],
         false,
     )]
     #[case(
-        GenotypeChoice::ComphetIndex,
+        RecessiveMode::CompoundHeterozygous,
         vec!["0/1,0/1,0/0","0/1,0/0,0/1"],
         true,
     )]
     #[case(
-        GenotypeChoice::RecessiveIndex,
+        RecessiveMode::Any,
         vec!["1/1,0/0,0/0","0/1,0/0,0/1"],
         true,
     )]
     #[case(
-        GenotypeChoice::RecessiveIndex,
+        RecessiveMode::Any,
         vec!["1/0,1/0,0/0","0/1,0/0,0/1"],
         true,
     )]
     #[case(
-        GenotypeChoice::RecessiveIndex,
+        RecessiveMode::Any,
         vec!["1/0,1/0,0/0","1/0,0/1,0/0"],
         false,
     )]
     fn passes_for_gene_full_trio(
-        #[case] gt_choice_index: GenotypeChoice,
+        #[case] recessive_mode: RecessiveMode,
         #[case] trio_gts: Vec<&str>,
         #[case] passes: bool,
     ) -> Result<(), anyhow::Error> {
+        use crate::seqvars::query::schema::query::{QuerySettingsGenotype, SampleGenotypeChoice};
+
         let query = CaseQuery {
-            genotype: vec![
-                ("index".into(), Some(gt_choice_index)),
-                ("father".into(), Some(GenotypeChoice::RecessiveParent)),
-                ("mother".into(), Some(GenotypeChoice::RecessiveParent)),
-            ]
-            .into_iter()
-            .collect(),
+            genotype: QuerySettingsGenotype {
+                recessive_mode,
+                sample_genotypes: indexmap::indexmap! {
+                    String::from("index") => SampleGenotypeChoice { sample: String::from("index"), genotype: GenotypeChoice::RecessiveIndex, ..Default::default() },
+                    String::from("father") => SampleGenotypeChoice { sample: String::from("father"), genotype: GenotypeChoice::RecessiveParent, ..Default::default() },
+                    String::from("mother") => SampleGenotypeChoice { sample: String::from("mother"), genotype: GenotypeChoice::RecessiveParent, ..Default::default() },
+                },
+            },
             ..Default::default()
         };
         let seqvars = trio_gts
             .iter()
             .map(|gts| {
                 let gts: Vec<&str> = gts.split(',').collect();
-                SequenceVariant {
-                    call_info: vec![
-                        (
-                            String::from("index"),
+                VariantRecord {
+                    call_infos: indexmap::indexmap! {
+                        String::from("index") =>
                             CallInfo {
+                                sample: String::from("index"),
                                 genotype: Some(gts[0].into()),
                                 ..Default::default()
                             },
-                        ),
-                        (
-                            String::from("father"),
+                        String::from("father") =>
                             CallInfo {
                                 genotype: Some(gts[1].into()),
                                 ..Default::default()
                             },
-                        ),
-                        (
-                            String::from("mother"),
+                        String::from("mother") =>
                             CallInfo {
                                 genotype: Some(gts[2].into()),
                                 ..Default::default()
                             },
-                        ),
-                    ]
-                    .into_iter()
-                    .collect(),
+                    },
                     ..Default::default()
                 }
             })
diff --git a/src/seqvars/query/output/call_related.rs b/src/seqvars/query/output/call_related.rs
index e9162120..e68c78c4 100644
--- a/src/seqvars/query/output/call_related.rs
+++ b/src/seqvars/query/output/call_related.rs
@@ -1,6 +1,6 @@
 //! Call-related information.
 
-use crate::seqvars::query::schema::SequenceVariant;
+use crate::seqvars::query::schema::data::VariantRecord;
 
 /// Call-related record.
 #[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)]
@@ -10,15 +10,15 @@ pub struct Record {
 }
 
 impl Record {
-    /// Construct a new `Record` from a `SequenceVariant`.
+    /// Construct a new `Record` from a `VariantRecord`.
     ///
     /// # Error
     ///
-    /// Returns an error if the `SequenceVariant` does not contain all necessary information.
-    pub fn with_seqvar(seqvar: &SequenceVariant) -> Result<Self, anyhow::Error> {
+    /// Returns an error if the `VariantRecord` does not contain all necessary information.
+    pub fn with_seqvar(seqvar: &VariantRecord) -> Result<Self, anyhow::Error> {
         Ok(Self {
             call_info: seqvar
-                .call_info
+                .call_infos
                 .iter()
                 .map(|(sample_name, call_info)| {
                     (
diff --git a/src/seqvars/query/output/gene_related.rs b/src/seqvars/query/output/gene_related.rs
index b29ecf88..3887fa9c 100644
--- a/src/seqvars/query/output/gene_related.rs
+++ b/src/seqvars/query/output/gene_related.rs
@@ -2,7 +2,7 @@
 
 use mehari::annotate::seqvars::ann::Consequence;
 
-use crate::seqvars::query::{annonars::Annotator, schema::SequenceVariant};
+use crate::seqvars::query::{annonars::Annotator, schema::data::VariantRecord};
 
 /// Gene-related information for a `ResultPayload`.
 #[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)]
@@ -20,16 +20,16 @@ pub struct Record {
 }
 
 impl Record {
-    /// Construct given a `SequenceVariant` if the information is given in the annotation.
+    /// Construct given a `VariantRecord` if the information is given in the annotation.
     ///
     /// Note that we will only look at the first annotation record as the ingest creates
-    /// one `SequenceVariant` record per gene.
+    /// one `VariantRecord` record per gene.
     ///
     /// # Error
     ///
     /// Returns an error if `seqvar` does not contain all necessary information.
     pub fn with_seqvar_and_annotator(
-        seqvar: &SequenceVariant,
+        seqvar: &VariantRecord,
         annotator: &Annotator,
     ) -> Result<Option<Self>, anyhow::Error> {
         if let Some(ann) = seqvar.ann_fields.first() {
diff --git a/src/seqvars/query/output/variant_related.rs b/src/seqvars/query/output/variant_related.rs
index 6359f663..22459433 100644
--- a/src/seqvars/query/output/variant_related.rs
+++ b/src/seqvars/query/output/variant_related.rs
@@ -7,7 +7,7 @@ use crate::seqvars::query::{
     output::variant_related::score_collection::{
         Collector, ExtremalValueCollector, SingleValueCollector,
     },
-    schema::SequenceVariant,
+    schema::data::{Ac as _, Af as _, An as _, Hemi as _, VariantRecord},
 };
 
 /// Helper modules for score collection.
@@ -153,7 +153,7 @@ pub struct Record {
 impl Record {
     /// Construct given sequence variant and annonars annotator.
     pub fn with_seqvar_and_annotator(
-        seqvar: &SequenceVariant,
+        seqvar: &VariantRecord,
         annotator: &Annotator,
     ) -> Result<Self, anyhow::Error> {
         Ok(Self {
@@ -166,7 +166,7 @@ impl Record {
 
     /// Query precomputed scores for `seqvar` from annonars `annotator`.
     pub fn query_precomputed_scores(
-        seqvar: &SequenceVariant,
+        seqvar: &VariantRecord,
         annotator: &Annotator,
     ) -> Result<indexmap::IndexMap<String, serde_json::Value>, anyhow::Error> {
         let mut result = indexmap::IndexMap::new();
@@ -269,7 +269,7 @@ pub struct DbIds {
 impl DbIds {
     /// Construct given sequence variant and annonars annotator.
     pub fn with_seqvar_and_annotator(
-        seqvar: &SequenceVariant,
+        seqvar: &VariantRecord,
         annotator: &Annotator,
     ) -> Result<Self, anyhow::Error> {
         Ok(Self {
@@ -300,7 +300,7 @@ pub struct Clinvar {
 impl Clinvar {
     /// Construct given sequence variant and annonars annotator.
     pub fn with_seqvar_and_annotator(
-        seqvar: &SequenceVariant,
+        seqvar: &VariantRecord,
         annotator: &Annotator,
     ) -> Result<Option<Self>, anyhow::Error> {
         let record = annotator
@@ -391,27 +391,27 @@ pub struct Frequency {
 
 impl Frequency {
     /// Extract frequency information from `seqvar`
-    pub fn with_seqvar(seqvar: &SequenceVariant) -> Result<Frequency, anyhow::Error> {
-        let chrom = annonars::common::cli::canonicalize(&seqvar.chrom);
+    pub fn with_seqvar(seqvar: &VariantRecord) -> Result<Frequency, anyhow::Error> {
+        let chrom = annonars::common::cli::canonicalize(&seqvar.vcf_variant.chrom);
         let frequency = if chrom == "MT" {
             FrequencyBuilder::default()
                 .gnomad_genomes(
                     NuclearFrequency::new(
-                        seqvar.gnomad_genomes_af(),
-                        seqvar.population_frequencies.gnomad.genomes_an,
-                        seqvar.population_frequencies.gnomad.genomes_het,
-                        seqvar.population_frequencies.gnomad.genomes_hom,
-                        seqvar.population_frequencies.gnomad.genomes_hemi,
+                        seqvar.population_frequencies.gnomad_genomes.af(),
+                        seqvar.population_frequencies.gnomad_genomes.an(),
+                        seqvar.population_frequencies.gnomad_genomes.het(),
+                        seqvar.population_frequencies.gnomad_genomes.hom(),
+                        seqvar.population_frequencies.gnomad_genomes.hemi(),
                     )
                     .some_unless_empty(),
                 )
                 .gnomad_exomes(
                     NuclearFrequency::new(
-                        seqvar.gnomad_exomes_af(),
-                        seqvar.population_frequencies.gnomad.exomes_an,
-                        seqvar.population_frequencies.gnomad.exomes_het,
-                        seqvar.population_frequencies.gnomad.exomes_hom,
-                        seqvar.population_frequencies.gnomad.exomes_hemi,
+                        seqvar.population_frequencies.gnomad_exomes.af(),
+                        seqvar.population_frequencies.gnomad_exomes.an(),
+                        seqvar.population_frequencies.gnomad_exomes.het(),
+                        seqvar.population_frequencies.gnomad_exomes.hom(),
+                        seqvar.population_frequencies.gnomad_exomes.hemi(),
                     )
                     .some_unless_empty(),
                 )
@@ -420,19 +420,19 @@ impl Frequency {
             FrequencyBuilder::default()
                 .gnomad_mtdna(
                     MtdnaFrequency::new(
-                        seqvar.gnomad_genomes_af(),
-                        seqvar.population_frequencies.gnomad.genomes_an,
-                        seqvar.population_frequencies.gnomad.genomes_het,
-                        seqvar.population_frequencies.gnomad.genomes_hom,
+                        seqvar.population_frequencies.gnomad_mt.af(),
+                        seqvar.population_frequencies.gnomad_mt.ac(),
+                        seqvar.population_frequencies.gnomad_mt.het(),
+                        seqvar.population_frequencies.gnomad_mt.hom(),
                     )
                     .some_unless_empty(),
                 )
                 .helixmtdb(
                     MtdnaFrequency::new(
-                        seqvar.helixmtdb_af(),
-                        seqvar.population_frequencies.helixmtdb.an,
-                        seqvar.population_frequencies.helixmtdb.het,
-                        seqvar.population_frequencies.helixmtdb.hom,
+                        seqvar.population_frequencies.helixmtdb.af(),
+                        seqvar.population_frequencies.helixmtdb.ac(),
+                        seqvar.population_frequencies.helixmtdb.het(),
+                        seqvar.population_frequencies.helixmtdb.hom(),
                     )
                     .some_unless_empty(),
                 )
diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs
deleted file mode 100644
index 0329b19b..00000000
--- a/src/seqvars/query/schema.rs
+++ /dev/null
@@ -1,1016 +0,0 @@
-//! Supporting code for seqvar query definition.
-
-use indexmap::IndexMap;
-use mehari::annotate::seqvars::ann;
-use noodles::vcf;
-use strum::IntoEnumIterator;
-
-use crate::common::genotype_to_string;
-
-/// Enumeration for recessive mode queries.
-#[derive(
-    serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Hash, Debug, Clone, Copy,
-)]
-#[serde(rename_all = "kebab-case")]
-pub enum RecessiveMode {
-    /// Recessive.
-    Recessive,
-    /// Compound recessive.
-    CompoundRecessive,
-}
-
-/// Choice for genotype.
-#[derive(
-    serde::Serialize,
-    serde::Deserialize,
-    PartialEq,
-    Eq,
-    PartialOrd,
-    Ord,
-    Hash,
-    Debug,
-    Clone,
-    Copy,
-    Default,
-    strum::EnumIter,
-)]
-#[serde(rename_all = "kebab-case")]
-pub enum GenotypeChoice {
-    /// Any genotype.
-    #[default]
-    Any,
-    /// Ref. genotype.
-    Ref,
-    /// Het. genotype.
-    Het,
-    /// Hom. genotype.
-    Hom,
-    /// Non-hom. genotype.
-    NonHom,
-    /// Variant genotype.
-    Variant,
-    /// Index in comp. het. recessive inheritance.
-    ComphetIndex,
-    /// Index in recessive inheritance.
-    RecessiveIndex,
-    /// Parent in recessive inheritance.
-    RecessiveParent,
-}
-
-impl GenotypeChoice {
-    /// Return wehther the genotype choice matches the genotype string.
-    ///
-    /// Note that we assume properly ingested VCFs with only one alternate allele.
-    /// The valid genotype strings have the form "<VAL>/<VAL>", "<VAL>|<VAL>" or
-    /// "<VAL>" with "<VAL>" being one of "0", "1", and ".".
-    pub fn matches(&self, gt_str: &str) -> Result<bool, anyhow::Error> {
-        let gt_str = if gt_str.starts_with('/') || gt_str.starts_with('|') {
-            &gt_str[1..]
-        } else {
-            gt_str
-        };
-        Ok(match self {
-            GenotypeChoice::Any => true,
-            GenotypeChoice::Ref => ["0", "0|0", "0/0"].contains(&gt_str),
-            GenotypeChoice::Het => ["0/1", "0|1", "1/0", "1|0"].contains(&gt_str),
-            GenotypeChoice::Hom => ["1", "1/1", "1|1"].contains(&gt_str),
-            GenotypeChoice::NonHom => !["1", "1/1", "1|1"].contains(&gt_str),
-            GenotypeChoice::Variant => {
-                ["1", "0/1", "0|1", "1/0", "1|0", "1|1", "1/1"].contains(&gt_str)
-            }
-            GenotypeChoice::ComphetIndex
-            | GenotypeChoice::RecessiveIndex
-            | GenotypeChoice::RecessiveParent => {
-                anyhow::bail!("recessive marker is not a genotype choice")
-            }
-        })
-    }
-}
-
-/// Choices for failing quality thresholds on genotypes.
-#[derive(
-    serde::Serialize,
-    serde::Deserialize,
-    PartialEq,
-    Eq,
-    PartialOrd,
-    Ord,
-    Hash,
-    Debug,
-    Clone,
-    Copy,
-    Default,
-    strum::EnumIter,
-)]
-#[serde(rename_all = "kebab-case")]
-pub enum FailFilterChoice {
-    /// Ignore failure.
-    #[default]
-    Ignore,
-    /// Drop whole variant.
-    #[serde(rename = "drop-variant")]
-    Drop,
-}
-
-/// Quality settings for one sample.
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
-pub struct SampleQualitySettings {
-    /// Weather to ignore or drop the whole variant on failure
-    pub filter_active: FailFilterChoice,
-    /// Minimal coverage for het. sites.
-    pub dp_het: Option<i32>,
-    /// Minimal coverage for hom. sites.
-    pub dp_hom: Option<i32>,
-    /// Minimal genotype quality.
-    pub gq: Option<i32>,
-    /// Minimal allele balance for het. variants.
-    pub ab: Option<f32>,
-    /// Minimal number of alternate reads.
-    pub ad: Option<i32>,
-    /// Maximal number of alternate reads
-    pub ad_max: Option<i32>,
-}
-
-impl From<crate::pbs::seqvars::SampleQualitySettings> for SampleQualitySettings {
-    fn from(old: crate::pbs::seqvars::SampleQualitySettings) -> Self {
-        Self {
-            filter_active: if old.filter_active {
-                FailFilterChoice::Drop
-            } else {
-                FailFilterChoice::Ignore
-            },
-            dp_het: old.dp_het,
-            dp_hom: old.dp_hom,
-            gq: old.gq,
-            ab: old.ab,
-            ad: old.ad,
-            ad_max: old.ad_max,
-        }
-    }
-}
-
-/// Data structure to hold a range.
-#[derive(
-    serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Hash, Debug, Clone,
-)]
-pub struct Range {
-    /// Start of range.
-    pub start: i32,
-    /// End of range.
-    pub end: i32,
-}
-
-impl From<crate::pbs::seqvars::Range> for Range {
-    fn from(value: crate::pbs::seqvars::Range) -> Self {
-        Self {
-            start: value.start,
-            end: value.end,
-        }
-    }
-}
-
-/// Data struture to hold a genomic region.
-#[derive(
-    serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Hash, Debug, Clone,
-)]
-pub struct GenomicRegion {
-    /// Chromosome.
-    pub chrom: String,
-    /// Range of region.
-    pub range: Option<Range>,
-}
-
-impl From<crate::pbs::seqvars::GenomicRegion> for GenomicRegion {
-    fn from(other: crate::pbs::seqvars::GenomicRegion) -> Self {
-        Self {
-            chrom: other.chrom,
-            range: other.range.map(Range::from),
-        }
-    }
-}
-
-serde_with::with_prefix!(prefix_clinvar "clinvar_");
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
-#[serde(default)]
-pub struct ClinVarOptions {
-    /// Whether to include benign ClinVar variants.
-    pub include_benign: bool,
-    /// Whether to include pathogenic ClinVar variants.
-    pub include_pathogenic: bool,
-    /// Whether to include likely benign ClinVar variants.
-    pub include_likely_benign: bool,
-    /// Whether to include likely pathogenic ClinVar variants.
-    pub include_likely_pathogenic: bool,
-    /// Whether to include uncertain significance ClinVar variants.
-    pub include_uncertain_significance: bool,
-    /// Whether to include conflicting interpretation ClinVar variants.
-    pub include_conflicting_classifications: bool,
-}
-
-impl From<crate::pbs::seqvars::ClinVarOptions> for ClinVarOptions {
-    fn from(other: crate::pbs::seqvars::ClinVarOptions) -> Self {
-        Self {
-            include_benign: other.include_benign,
-            include_pathogenic: other.include_pathogenic,
-            include_likely_benign: other.include_likely_benign,
-            include_likely_pathogenic: other.include_likely_pathogenic,
-            include_uncertain_significance: other.include_uncertain_significance,
-            include_conflicting_classifications: other.include_conflicting_classifications,
-        }
-    }
-}
-
-serde_with::with_prefix!(prefix_inhouse "inhouse_");
-#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
-#[serde(default)]
-pub struct InhouseFrequencyOptions {
-    /// Whether to enable filtration by 1000 Genomes.
-    pub enabled: bool,
-    /// Maximal number of in-house carriers
-    pub carriers: Option<i32>,
-    /// Maximal number of in-house heterozygous carriers
-    pub heterozygous: Option<i32>,
-    /// Maximal number of in-house homozygous carriers
-    pub homozygous: Option<i32>,
-    /// Maximal number of in-house hemizygous carriers
-    pub hemizygous: Option<i32>,
-}
-
-#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
-#[serde(default)]
-/// TODO: currently unused?
-pub struct GnomadNuclearOptions {
-    /// Whether to enable filtration by 1000 Genomes.
-    pub enabled: bool,
-    /// Maximal number of in-house carriers.
-    pub carriers: Option<i32>,
-    /// Maximal number of in-house heterozygous carriers.
-    pub heterozygous: Option<i32>,
-    /// Maximal number of in-house homozygous carriers.
-    pub homozygous: Option<i32>,
-    /// Maximal number of in-house hemizygous carriers.
-    pub hemizygous: Option<i32>,
-    // Maximal allele frequency.
-    #[serde(rename = "frequency")]
-    pub allele_frequency: Option<f32>,
-}
-
-impl From<crate::pbs::seqvars::GnomadNuclearOptions> for GnomadNuclearOptions {
-    fn from(other: crate::pbs::seqvars::GnomadNuclearOptions) -> Self {
-        Self {
-            enabled: other.enabled,
-            carriers: other.carriers,
-            heterozygous: other.heterozygous,
-            homozygous: other.homozygous,
-            hemizygous: other.hemizygous,
-            allele_frequency: other.allele_frequency,
-        }
-    }
-}
-
-impl From<crate::pbs::seqvars::InhouseFrequencyOptions> for InhouseFrequencyOptions {
-    fn from(other: crate::pbs::seqvars::InhouseFrequencyOptions) -> Self {
-        Self {
-            enabled: other.enabled,
-            carriers: other.carriers,
-            heterozygous: other.heterozygous,
-            homozygous: other.homozygous,
-            hemizygous: other.hemizygous,
-        }
-    }
-}
-
-#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
-#[serde(default)]
-pub struct GnomadMitochondrialOptions {
-    /// Whether to enable filtration by 1000 Genomes.
-    pub enabled: bool,
-    /// Maximal number of carriers
-    pub carriers: Option<i32>,
-    /// Maximal number of heteroplasmic carriers.
-    pub heteroplasmic: Option<i32>,
-    /// Maximal number of homoplasmic carriers.
-    pub homoplasmic: Option<i32>,
-    /// Maximal allele frequency.
-    #[serde(rename = "frequency")]
-    pub allele_frequency: Option<f32>,
-}
-
-impl From<crate::pbs::seqvars::GnomadMitochondrialOptions> for GnomadMitochondrialOptions {
-    fn from(other: crate::pbs::seqvars::GnomadMitochondrialOptions) -> Self {
-        Self {
-            enabled: other.enabled,
-            carriers: other.carriers,
-            heteroplasmic: other.heteroplasmic,
-            homoplasmic: other.homoplasmic,
-            allele_frequency: other.allele_frequency,
-        }
-    }
-}
-
-serde_with::with_prefix!(prefix_helixmtdb "helixmtdb_");
-#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
-#[serde(default)]
-/// TODO: currently unused?
-pub struct HelixMtDbOptions {
-    /// Whether to enable filtration by mtDB.
-    pub enabled: bool,
-    /// Maximal frequency in HelixMtDb
-    pub frequency: Option<f32>,
-    /// Maximal number of heterozygous carriers in HelixMtDb.
-    pub heteroplasmic: Option<i32>,
-    /// Maximal number of homozygous carriers in HelixMtDb.
-    pub homoplasmic: Option<i32>,
-}
-
-impl From<crate::pbs::seqvars::HelixMtDbOptions> for HelixMtDbOptions {
-    fn from(other: crate::pbs::seqvars::HelixMtDbOptions) -> Self {
-        Self {
-            enabled: other.enabled,
-            frequency: other.frequency,
-            heteroplasmic: other.heteroplasmic,
-            homoplasmic: other.homoplasmic,
-        }
-    }
-}
-
-serde_with::with_prefix!(prefix_gnomad_exomes "gnomad_exomes_");
-serde_with::with_prefix!(prefix_gnomad_genomes "gnomad_genomes_");
-serde_with::with_prefix!(prefix_gnomad_mt "gnomat_mt_");
-#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
-#[serde(default)]
-pub struct PopulationFrequencyOptions {
-    #[serde(flatten, with = "prefix_gnomad_exomes")]
-    pub gnomad_exomes: GnomadNuclearOptions,
-    #[serde(flatten, with = "prefix_gnomad_genomes")]
-    pub gnomad_genomes: GnomadNuclearOptions,
-    // gnomAD-MT filter
-    #[serde(flatten, with = "prefix_gnomad_mt")]
-    pub gnomad_mt: GnomadMitochondrialOptions,
-    #[serde(flatten, with = "prefix_helixmtdb")]
-    pub helixmtdb: HelixMtDbOptions,
-}
-
-impl From<crate::pbs::seqvars::PopulationFrequencyOptions> for PopulationFrequencyOptions {
-    fn from(other: crate::pbs::seqvars::PopulationFrequencyOptions) -> Self {
-        Self {
-            gnomad_exomes: other
-                .gnomad_exomes
-                .map(GnomadNuclearOptions::from)
-                .unwrap_or_default(),
-            gnomad_genomes: other
-                .gnomad_genomes
-                .map(GnomadNuclearOptions::from)
-                .unwrap_or_default(),
-            gnomad_mt: other
-                .gnomad_mt
-                .map(GnomadMitochondrialOptions::from)
-                .unwrap_or_default(),
-            helixmtdb: other
-                .helixmtdb
-                .map(HelixMtDbOptions::from)
-                .unwrap_or_default(),
-        }
-    }
-}
-
-serde_with::with_prefix!(prefix_var_type "var_type_");
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
-#[serde(default)]
-pub struct VariantTypeOptions {
-    /// Whether to include SNVs.
-    pub snv: bool,
-    /// Whether to include indels.
-    pub indel: bool,
-    /// Whether to include MNVs.
-    pub mnv: bool,
-}
-
-impl Default for VariantTypeOptions {
-    fn default() -> Self {
-        VariantTypeOptions {
-            snv: true,
-            indel: true,
-            mnv: true,
-        }
-    }
-}
-
-impl From<crate::pbs::seqvars::VariantTypeOptions> for VariantTypeOptions {
-    fn from(other: crate::pbs::seqvars::VariantTypeOptions) -> Self {
-        Self {
-            snv: other.snv,
-            indel: other.indel,
-            mnv: other.mnv,
-        }
-    }
-}
-
-#[derive(serde::Serialize, serde::Deserialize, Default, PartialEq, Debug, Clone)]
-#[serde(default)]
-pub struct LocusRelatedOptions {
-    /// List of HGNC symbols, HGNC:<ID>s, ENSG<ID>s, or NCBI Gene IDs to restrict
-    /// the resulting variants to.
-    pub gene_allowlist: Option<Vec<String>>,
-    /// List of genomic regions to limit restrict the resulting variants to.
-    pub genomic_regions: Option<Vec<GenomicRegion>>,
-}
-
-impl From<crate::pbs::seqvars::LocusRelatedOptions> for LocusRelatedOptions {
-    fn from(other: crate::pbs::seqvars::LocusRelatedOptions) -> Self {
-        Self {
-            gene_allowlist: match other.gene_allowlist.first() {
-                None => None,
-                _ => Some(other.gene_allowlist),
-            },
-            genomic_regions: match other.genomic_regions.first() {
-                None => None,
-                _ => Some(
-                    other
-                        .genomic_regions
-                        .iter()
-                        .map(std::borrow::ToOwned::to_owned)
-                        .map(GenomicRegion::from)
-                        .collect(),
-                ),
-            },
-        }
-    }
-}
-
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
-#[serde(default)]
-pub struct TranscriptOptions {
-    /// Whether to include coding transcripts.
-    pub transcripts_coding: bool,
-    /// Whether to include non-coding transcripts.
-    pub transcripts_noncoding: bool,
-    /// Maximal distance to next exon, if any.
-    pub max_exon_dist: Option<i32>,
-}
-
-impl From<crate::pbs::seqvars::TranscriptOptions> for TranscriptOptions {
-    fn from(other: crate::pbs::seqvars::TranscriptOptions) -> Self {
-        Self {
-            transcripts_coding: other.transcripts_coding,
-            transcripts_noncoding: other.transcripts_noncoding,
-            max_exon_dist: other.max_exon_dist,
-        }
-    }
-}
-
-impl Default for TranscriptOptions {
-    fn default() -> Self {
-        TranscriptOptions {
-            transcripts_coding: true,
-            transcripts_noncoding: true,
-            max_exon_dist: Default::default(),
-        }
-    }
-}
-
-/// Data structure with a single query.
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)]
-#[serde(default)]
-pub struct CaseQuery {
-    /// Molecular consequences to consider.
-    pub consequences: Vec<mehari::annotate::seqvars::ann::Consequence>,
-
-    /// Quality settings for each individual.
-    pub quality: indexmap::IndexMap<String, SampleQualitySettings>,
-
-    /// Genotype choice for each individual.
-    pub genotype: indexmap::IndexMap<String, Option<GenotypeChoice>>,
-    #[serde(flatten)]
-    pub transcript: TranscriptOptions,
-    #[serde(flatten, with = "prefix_var_type")]
-    pub var_type: VariantTypeOptions,
-    #[serde(flatten)]
-    pub locus: LocusRelatedOptions,
-
-    // In protobuf this lives inside ClinVarOptions
-    /// Wether to require ClinVar membership.
-    pub require_in_clinvar: bool,
-    /// ClinVar related filter options.
-    #[serde(flatten, with = "prefix_clinvar")]
-    pub clinvar: ClinVarOptions,
-
-    /// PopulationFrequency related filter options
-    #[serde(flatten)]
-    pub population_frequency: PopulationFrequencyOptions,
-
-    /// Inhouse related filter options.
-    #[serde(flatten, with = "prefix_inhouse")]
-    pub inhouse: InhouseFrequencyOptions,
-}
-
-impl From<crate::pbs::seqvars::CaseQuery> for CaseQuery {
-    fn from(other: crate::pbs::seqvars::CaseQuery) -> Self {
-        let consequences: Vec<_> = other
-            .consequences
-            .iter()
-            .map(|x| ann::Consequence::iter().nth(*x as usize).unwrap())
-            .collect();
-        let quality: IndexMap<String, SampleQualitySettings> = other
-            .quality
-            .iter()
-            .map(|(x, y)| (x.to_owned(), y.clone().into()))
-            .collect();
-
-        Self {
-            consequences,
-            quality,
-            genotype: other
-                .genotype
-                .iter()
-                .map(|(x, y)| (x.to_owned(), GenotypeChoice::iter().nth(*y as usize)))
-                .collect(),
-
-            transcript: other
-                .transcript
-                .map(TranscriptOptions::from)
-                .unwrap_or_default(),
-            var_type: other
-                .var_type
-                .map(VariantTypeOptions::from)
-                .unwrap_or_default(),
-            locus: other
-                .locus
-                .map(LocusRelatedOptions::from)
-                .unwrap_or_default(),
-            require_in_clinvar: other.clinvar.clone().unwrap_or_default().require_in_clinvar,
-            clinvar: other.clinvar.map(ClinVarOptions::from).unwrap_or_default(),
-            population_frequency: other
-                .population_frequency
-                .map(PopulationFrequencyOptions::from)
-                .unwrap_or_default(),
-            inhouse: other
-                .inhouse
-                .map(InhouseFrequencyOptions::from)
-                .unwrap_or_default(),
-        }
-    }
-}
-
-impl Default for ClinVarOptions {
-    fn default() -> Self {
-        Self {
-            include_benign: true,
-            include_pathogenic: true,
-            include_likely_benign: true,
-            include_likely_pathogenic: true,
-            include_uncertain_significance: true,
-            include_conflicting_classifications: true,
-        }
-    }
-}
-
-impl Default for CaseQuery {
-    /// Returns default values for a `CaseQuery` which makes all variants pass.
-    fn default() -> Self {
-        Self {
-            consequences: mehari::annotate::seqvars::ann::Consequence::all(),
-            population_frequency: Default::default(),
-            quality: Default::default(),
-            genotype: Default::default(),
-            transcript: Default::default(),
-            var_type: Default::default(),
-            locus: Default::default(),
-            require_in_clinvar: Default::default(),
-            clinvar: Default::default(),
-            inhouse: Default::default(),
-        }
-    }
-}
-
-impl CaseQuery {
-    /// Return whether recessive mode has been enabled.
-    pub fn recessive_mode(&self) -> bool {
-        self.genotype.values().any(|gt_choice| {
-            matches!(
-                gt_choice,
-                Some(
-                    GenotypeChoice::ComphetIndex
-                        | GenotypeChoice::RecessiveIndex
-                        | GenotypeChoice::RecessiveParent
-                )
-            )
-        })
-    }
-
-    /// Returns name of the recessive index sample.
-    pub fn index_sample(&self) -> Option<String> {
-        for (name, gt_choice) in &self.genotype {
-            match gt_choice {
-                Some(GenotypeChoice::ComphetIndex | GenotypeChoice::RecessiveIndex) => {
-                    return Some(name.clone())
-                }
-                _ => continue,
-            }
-        }
-
-        None
-    }
-}
-/// Information on the call as written out by ingest.
-///
-/// Note that the ingested files have exactly one alternate allele.
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
-pub struct CallInfo {
-    /// The genotype, if applicable, e.g., "0/1"
-    pub genotype: Option<String>,
-    /// Genotype quality score, if applicable
-    pub quality: Option<f32>,
-    /// Total read coverage at site in the sample.
-    pub dp: Option<i32>,
-    /// Alternate allele depth for the single allele in the sample.
-    pub ad: Option<i32>,
-    /// Physical phasing ID for this sample.
-    pub phasing_id: Option<i32>,
-}
-
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
-pub struct Gnomads {
-    /// Number of alleles in gnomAD exomes (not for chrMT).
-    pub exomes_an: i32,
-    /// Number of homozygous carriers in gnomAD exomes (not for chrMT).
-    pub exomes_hom: i32,
-    /// Number of heterozygous carriers in gnomAD exomes (not for chrMT).
-    pub exomes_het: i32,
-    /// Number of hemizygous carriers in gnomAD exomes (not for chrMT).
-    pub exomes_hemi: i32,
-
-    /// Number of alleles in gnomAD genomes (also for chrMT).
-    pub genomes_an: i32,
-    /// Number of homozygous carriers in gnomAD genomes (also for chrMT).
-    pub genomes_hom: i32,
-    /// Number of heterozygous carriers in gnomAD genomes (also for chrMT).
-    pub genomes_het: i32,
-    /// Number of hemizygous carriers in gnomAD genomes (not for chrMT).
-    pub genomes_hemi: i32,
-}
-
-// Name difference due to legacy json
-serde_with::with_prefix!(prefix_helix "helix_");
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
-pub struct HelixMtDBs {
-    /// Number of alleles in HelixMtDb cohort (only chrMT).
-    pub an: i32,
-    /// Number of homoplasmic carriers in HelixMtDb cohort (only chrMT).
-    pub hom: i32,
-    /// Number of heteroplasmic carriers in HelixMtDb cohort (only chrMT).
-    pub het: i32,
-}
-
-serde_with::with_prefix!(prefix_gnomad "gnomad_");
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
-
-pub struct PopulationFrequencies {
-    #[serde(flatten, with = "prefix_gnomad")]
-    pub gnomad: Gnomads,
-    #[serde(flatten, with = "prefix_helix")]
-    pub helixmtdb: HelixMtDBs,
-}
-
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
-pub struct InhouseFrequencies {
-    /// Number of in-house alleles (also for chrMT).
-    pub an: i32,
-    /// Number of homozygous carriers in in-house cohort (also for chrMT).
-    pub hom: i32,
-    /// Number of heterozygous carriers in in-house cohort (also for chrMT).
-    pub het: i32,
-    /// Number of hemizygous carriers in in-house cohort (not for chrMT).
-    pub hemi: i32,
-}
-
-/// Definition of a sequence variant with per-sample genotype calls.
-///
-/// This uses a subset/specialization of what is described by the VCF standard
-/// for the purpose of running SV queries in `varfish-server-worker`.
-#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)]
-pub struct SequenceVariant {
-    /// Chromosome name
-    pub chrom: String,
-    /// 1-based start position of the variant (or position on first chromosome
-    /// for break-ends)
-    pub pos: i32,
-    /// Reference allele.
-    pub reference: String,
-    /// Alternative allele.
-    pub alternative: String,
-
-    /// Variant effect annotation.
-    pub ann_fields: Vec<mehari::annotate::seqvars::ann::AnnField>,
-
-    /// Mapping of sample to genotype information for the SV.
-    pub call_info: indexmap::IndexMap<String, CallInfo>,
-
-    #[serde(flatten)]
-    pub population_frequencies: PopulationFrequencies,
-
-    #[serde(flatten, with = "prefix_inhouse")]
-    pub inhouse_frequencies: InhouseFrequencies,
-}
-
-impl SequenceVariant {
-    /// Convert from VCF record.
-    pub fn from_vcf(
-        record: &vcf::variant::RecordBuf,
-        header: &vcf::Header,
-    ) -> Result<Self, anyhow::Error> {
-        let chrom = record.reference_sequence_name().to_string();
-        let pos: usize = record.variant_start().expect("empty variant_start?").into();
-        let pos = pos as i32;
-
-        let reference = record.reference_bases().to_string();
-        let alternative = record
-            .alternate_bases()
-            .as_ref()
-            .iter()
-            .next()
-            .expect("no alternate base?")
-            .to_string();
-
-        let call_info = Self::build_call_info(record, header)?;
-        let ann_fields = Self::extract_ann_fields(record)?;
-
-        let result = Self {
-            chrom,
-            pos,
-            reference,
-            alternative,
-            call_info,
-            ann_fields,
-            ..Default::default()
-        };
-
-        Self::with_freqs(result, record)
-    }
-
-    /// Build call information.
-    fn build_call_info(
-        record: &vcf::variant::RecordBuf,
-        header: &vcf::Header,
-    ) -> Result<indexmap::IndexMap<String, CallInfo>, anyhow::Error> {
-        use vcf::variant::record::samples::keys::key;
-        let mut result = indexmap::IndexMap::new();
-
-        for (name, sample) in header.sample_names().iter().zip(record.samples().values()) {
-            let genotype = if let Some(Some(
-                vcf::variant::record_buf::samples::sample::value::Value::Genotype(gt),
-            )) = sample.get(key::GENOTYPE)
-            {
-                Some(genotype_to_string(&gt)?)
-            } else {
-                None
-            };
-            let quality = if let Some(Some(
-                vcf::variant::record_buf::samples::sample::value::Value::Integer(quality),
-            )) = sample.get(key::CONDITIONAL_GENOTYPE_QUALITY)
-            {
-                Some(*quality as f32)
-            } else {
-                None
-            };
-            let dp = if let Some(Some(
-                vcf::variant::record_buf::samples::sample::value::Value::Integer(dp),
-            )) = sample.get(key::READ_DEPTH)
-            {
-                Some(*dp)
-            } else {
-                None
-            };
-            let ad =
-                if let Some(Some(vcf::variant::record_buf::samples::sample::value::Value::Array(
-                    vcf::variant::record_buf::samples::sample::value::Array::Integer(ad),
-                ))) = sample.get(key::READ_DEPTHS)
-                {
-                    Some(ad[1].expect("empty AD?"))
-                } else {
-                    None
-                };
-            let phase_set = if let Some(Some(
-                vcf::variant::record_buf::samples::sample::value::Value::Integer(id),
-            )) = sample.get(key::PHASE_SET)
-            {
-                Some(*id)
-            } else {
-                None
-            };
-
-            result.insert(
-                name.clone(),
-                CallInfo {
-                    genotype,
-                    quality,
-                    dp,
-                    ad,
-                    phasing_id: phase_set,
-                },
-            );
-        }
-
-        Ok(result)
-    }
-
-    /// Extract `INFO/ANN` entries
-    fn extract_ann_fields(
-        record: &vcf::variant::RecordBuf,
-    ) -> Result<Vec<mehari::annotate::seqvars::ann::AnnField>, anyhow::Error> {
-        if let Some(Some(ann)) = record.info().get("ANN") {
-            if let vcf::variant::record_buf::info::field::Value::Array(
-                vcf::variant::record_buf::info::field::value::Array::String(ann),
-            ) = ann
-            {
-                ann.iter()
-                    .flatten()
-                    .map(|s| s.parse::<mehari::annotate::seqvars::ann::AnnField>())
-                    .collect::<Result<Vec<_>, _>>()
-                    .map_err(|e| anyhow::anyhow!("problem parsing ANN: {}", e))
-            } else {
-                anyhow::bail!("invalid type of INFO/ANN")
-            }
-        } else {
-            Ok(Vec::default())
-        }
-    }
-
-    /// Copy the frequencies from `record` to `result`.
-    fn with_freqs(
-        result: SequenceVariant,
-        record: &vcf::variant::RecordBuf,
-    ) -> Result<SequenceVariant, anyhow::Error> {
-        use vcf::variant::record_buf::info::field::Value;
-
-        macro_rules! extract_key {
-            ($key:ident) => {
-                let $key =
-                    if let Some(Some(Value::Integer($key))) = record.info().get(stringify!($key)) {
-                        *$key
-                    } else {
-                        0
-                    };
-            };
-        }
-
-        extract_key!(gnomad_exomes_an);
-        extract_key!(gnomad_exomes_hom);
-        extract_key!(gnomad_exomes_het);
-        extract_key!(gnomad_exomes_hemi);
-
-        extract_key!(gnomad_genomes_an);
-        extract_key!(gnomad_genomes_hom);
-        extract_key!(gnomad_genomes_het);
-        extract_key!(gnomad_genomes_hemi);
-
-        extract_key!(helix_an);
-        extract_key!(helix_hom);
-        extract_key!(helix_het);
-
-        Ok(SequenceVariant {
-            population_frequencies: PopulationFrequencies {
-                gnomad: Gnomads {
-                    exomes_an: gnomad_exomes_an,
-                    exomes_hom: gnomad_exomes_hom,
-                    exomes_het: gnomad_exomes_het,
-                    exomes_hemi: gnomad_exomes_hemi,
-
-                    genomes_an: gnomad_genomes_an,
-                    genomes_hom: gnomad_genomes_hom,
-                    genomes_het: gnomad_genomes_het,
-                    genomes_hemi: gnomad_genomes_hemi,
-                },
-                helixmtdb: HelixMtDBs {
-                    an: helix_an,
-                    hom: helix_hom,
-                    het: helix_het,
-                },
-            },
-            ..result
-        })
-    }
-
-    /// Return allele frequency in gnomAD exomes.
-    pub fn gnomad_exomes_af(&self) -> f32 {
-        if self.population_frequencies.gnomad.exomes_an == 0 {
-            return 0f32;
-        }
-        let an = self.population_frequencies.gnomad.exomes_an as f32;
-        let hom = self.population_frequencies.gnomad.exomes_hom as f32;
-        let het = self.population_frequencies.gnomad.exomes_het as f32;
-        let hemi = self.population_frequencies.gnomad.exomes_hemi as f32;
-        (2.0 * hom + het + hemi) / an
-    }
-
-    /// Return allele frequency in gnomAD genomes.
-    pub fn gnomad_genomes_af(&self) -> f32 {
-        if self.population_frequencies.gnomad.genomes_an == 0 {
-            return 0f32;
-        }
-
-        let an = self.population_frequencies.gnomad.genomes_an as f32;
-        let hom = self.population_frequencies.gnomad.genomes_hom as f32;
-        let het = self.population_frequencies.gnomad.genomes_het as f32;
-        let hemi = self.population_frequencies.gnomad.genomes_hemi as f32;
-        (2.0 * hom + het + hemi) / an
-    }
-
-    /// Return allele frequency in HelixMtDb.
-    pub fn helixmtdb_af(&self) -> f32 {
-        if self.population_frequencies.helixmtdb.an == 0 {
-            return 0f32;
-        }
-        let an = self.population_frequencies.helixmtdb.an as f32;
-        let hom = self.population_frequencies.helixmtdb.hom as f32;
-        let het = self.population_frequencies.helixmtdb.het as f32;
-        (2.0 * hom + het) / an
-    }
-}
-
-#[cfg(test)]
-pub mod test {
-    use noodles::vcf;
-    use rstest::rstest;
-
-    pub mod genotype_choice {
-        use super::super::GenotypeChoice::{self, *};
-        use rstest::rstest;
-
-        #[rstest]
-        #[case(Any, &["0", "0/0", "0|0", "1", "1/1", "1|1", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], true)]
-        #[case(Ref, &["0", "0/0", "0|0"], true)]
-        #[case(Ref, &[ "1", "1/1", "1|1", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], false)]
-        #[case(Het, &["0/1", "0|1", "1/0", "1|0"], true)]
-        #[case(Het, &["0", "0/0", "0|0", "1", "1/1", "1|1", ".", "./.", ".|."], false)]
-        #[case(Hom, &["1", "1/1", "1|1"], true)]
-        #[case(Hom, &["0", "0/0", "0|0", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], false)]
-        #[case(NonHom, &["1", "1/1", "1|1"], false)]
-        #[case(NonHom, &["0", "0/0", "0|0", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], true)]
-        #[case(Variant, &["1", "1/1", "1|1", "0/1",  "0|1",  "1/0", "1|0"], true)]
-        #[case(Variant, &["0", "0/0", "0|0", ".", "./.", ".|."], false)]
-        pub fn matches(
-            #[case] genotype_choice: GenotypeChoice,
-            #[case] gt_strs: &[&str],
-            #[case] expected: bool,
-        ) {
-            for gt_str in gt_strs {
-                assert_eq!(
-                    genotype_choice.matches(gt_str).unwrap(),
-                    expected,
-                    "{:?} {}",
-                    genotype_choice,
-                    gt_str
-                );
-            }
-        }
-    }
-
-    #[rstest]
-    #[case("tests/seqvars/query/empty")]
-    #[case("tests/seqvars/query/full")]
-    #[case("tests/seqvars/query/with_extra")]
-    pub fn smoke_test_load(#[case] path_input: &str) -> Result<(), anyhow::Error> {
-        mehari::common::set_snapshot_suffix!("{}.json", path_input.split('/').last().unwrap());
-
-        let query: super::CaseQuery =
-            serde_json::from_reader(std::fs::File::open(format!("{}.json", path_input))?)?;
-
-        if !path_input.contains("with_extra") {
-            // Check if pbjson loading yields same result
-            let query_pb: crate::pbs::seqvars::CaseQuery =
-                serde_json::from_reader(std::fs::File::open(format!("{}-pb.json", path_input))?)?;
-            let query_pb_conv = super::CaseQuery::from(query_pb);
-            assert_eq!(query, query_pb_conv);
-        }
-        insta::assert_yaml_snapshot!(&query);
-
-        Ok(())
-    }
-
-    #[rstest::rstest]
-    #[case("tests/seqvars/query/Case_1.ingested.vcf")]
-    #[case("tests/seqvars/query/dragen.ingested.vcf")]
-    pub fn sequence_variant_from_vcf(#[case] path_input: &str) -> Result<(), anyhow::Error> {
-        use noodles::vcf::variant::RecordBuf;
-
-        mehari::common::set_snapshot_suffix!("{}", path_input.split('/').last().unwrap());
-
-        let mut vcf_reader = vcf::io::reader::Builder::default()
-            .build_from_path(path_input)
-            .unwrap();
-        let header = vcf_reader.read_header()?;
-
-        for record in vcf_reader.records() {
-            let record = record?;
-            let seqvar = super::SequenceVariant::from_vcf(
-                &RecordBuf::try_from_variant_record(&header, &record)?,
-                &header,
-            )?;
-
-            insta::assert_yaml_snapshot!(&seqvar);
-        }
-
-        Ok(())
-    }
-}
diff --git a/src/seqvars/query/schema/data.rs b/src/seqvars/query/schema/data.rs
new file mode 100644
index 00000000..2b40e1fa
--- /dev/null
+++ b/src/seqvars/query/schema/data.rs
@@ -0,0 +1,714 @@
+//! Code for representing variants internally, corresponds to what is written
+//! out by `seqvars ingest`.
+
+use noodles::vcf;
+
+use crate::common::genotype_to_string;
+
+/// Trait for attempting conversion from VCF record.
+pub trait TryFromVcf: Sized {
+    /// Error type to use.
+    type Error;
+
+    /// Convert from VCF record.
+    ///
+    /// # Arguments
+    ///
+    /// * `record` - VCF record.
+    /// * `header` - VCF header.
+    ///
+    /// # Errors
+    ///
+    /// Returns an error if the record cannot be converted.
+    fn try_from_vcf(
+        record: &vcf::variant::RecordBuf,
+        header: &vcf::Header,
+    ) -> Result<Self, Self::Error>;
+}
+
+/// Information on the call as written out by ingest.
+///
+/// Corresponds to `FORMAT/*` in VCF.
+///
+/// Note that the ingested files have exactly one alternate allele.
+#[derive(Debug, Clone, Default, PartialEq, serde::Serialize, serde::Deserialize)]
+pub struct CallInfo {
+    /// The sample name.
+    pub sample: String,
+    /// The genotype, if applicable, e.g., "0/1"
+    pub genotype: Option<String>,
+    /// Genotype quality score, if applicable
+    pub quality: Option<f32>,
+    /// Total read coverage at site in the sample.
+    pub dp: Option<i32>,
+    /// Alternate allele depth for the single allele in the sample.
+    pub ad: Option<i32>,
+    /// Physical phasing ID for this sample.
+    pub phasing_id: Option<i32>,
+}
+
+impl Eq for CallInfo {}
+
+/// pub trait for total allele counts.
+pub trait An {
+    /// Number of covered alleles.
+    fn an(&self) -> i32;
+}
+
+/// pub trait for variant alternate allele counts.
+pub trait Ac {
+    /// Number of homozygous/homoplasmic carriers.
+    fn hom(&self) -> i32;
+    /// Number of heterozygous/heteroplasmic carriers.
+    fn het(&self) -> i32;
+    /// Number of total alternate alleles.
+    fn ac(&self) -> i32;
+}
+
+/// pub trait for allele frequency.
+pub trait Af {
+    /// Allele frequency.
+    fn af(&self) -> f32;
+}
+
+/// Blanket implementation of `Af` for any type that implements `Ac` and `An`.
+impl<T: Ac + An> Af for T {
+    fn af(&self) -> f32 {
+        if self.an() == 0 {
+            0.0
+        } else {
+            self.ac() as f32 / self.an() as f32
+        }
+    }
+}
+
+/// pub trait for carrier count.
+pub trait Carriers {
+    /// Total number of carriers.
+    fn carriers(&self) -> i32;
+}
+
+/// pub trait for nuclear variant alternate allele including hemizygous.
+pub trait Hemi: Ac {
+    /// Number of hemizygous carriers.
+    fn hemi(&self) -> i32;
+}
+
+/// gnomAD Population frequencies for variants on nuclear chromosomes.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct NuclearFrequencies {
+    /// Number of alleles.
+    pub an: i32,
+    /// Number of homozygous carriers.
+    pub hom: i32,
+    /// Number of heterozygous carriers.
+    pub het: i32,
+    /// Number of hemizygous carriers.
+    pub hemi: i32,
+}
+
+impl An for NuclearFrequencies {
+    fn an(&self) -> i32 {
+        self.an
+    }
+}
+
+impl Ac for NuclearFrequencies {
+    fn hom(&self) -> i32 {
+        self.hom
+    }
+    fn het(&self) -> i32 {
+        self.het
+    }
+    fn ac(&self) -> i32 {
+        2 * self.hom + self.het + self.hemi
+    }
+}
+
+impl Hemi for NuclearFrequencies {
+    fn hemi(&self) -> i32 {
+        self.hemi
+    }
+}
+
+impl Carriers for NuclearFrequencies {
+    fn carriers(&self) -> i32 {
+        self.hom + self.het + self.hemi
+    }
+}
+
+/// Population frequencies for variants on the mitochondrial chromosome.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct MitochondrialFrequencies {
+    /// Number of alleles.
+    pub an: i32,
+    /// Number of homoplasmic carriers.
+    pub hom: i32,
+    /// Number of heteroplasmic carriers.
+    pub het: i32,
+}
+
+impl An for MitochondrialFrequencies {
+    fn an(&self) -> i32 {
+        self.an
+    }
+}
+
+impl Ac for MitochondrialFrequencies {
+    fn hom(&self) -> i32 {
+        self.hom
+    }
+    fn het(&self) -> i32 {
+        self.het
+    }
+    fn ac(&self) -> i32 {
+        self.hom + self.het
+    }
+}
+
+impl Carriers for MitochondrialFrequencies {
+    fn carriers(&self) -> i32 {
+        self.hom + self.het
+    }
+}
+
+/// In-house frequencies.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct InHouseFrequencies {
+    /// Number of homozygous carriers.
+    pub hom: i32,
+    /// Number of heterozygous carriers.
+    pub het: i32,
+    /// Number of hemizygous carriers.
+    pub hemi: i32,
+    /// Total number of carriers.
+    pub total: i32,
+}
+
+impl Ac for InHouseFrequencies {
+    fn hom(&self) -> i32 {
+        self.hom
+    }
+    fn het(&self) -> i32 {
+        self.het
+    }
+    fn ac(&self) -> i32 {
+        2 * self.hom + self.het + self.hemi
+    }
+}
+
+impl An for InHouseFrequencies {
+    fn an(&self) -> i32 {
+        self.total
+    }
+}
+
+impl Carriers for InHouseFrequencies {
+    fn carriers(&self) -> i32 {
+        2 * self.hom + self.het + self.hemi
+    }
+}
+
+/// Population frequencies for a variant.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct PopulationFrequencies {
+    /// Frequencies in gnomAD-exomes.
+    pub gnomad_exomes: NuclearFrequencies,
+    /// Frequencies in gnomAD-genomes.
+    pub gnomad_genomes: NuclearFrequencies,
+    /// Frequencies in gnomAD-MT.
+    pub gnomad_mt: MitochondrialFrequencies,
+    /// Frequencies in HelixMtDb.
+    pub helixmtdb: MitochondrialFrequencies,
+    /// Frequencies in In-house database.
+    pub inhouse: InHouseFrequencies,
+}
+
+/// Supporting code for `PopulationFrequencies`.
+pub(crate) mod population_frequencies {
+    /// Error type for `FromVcf` implementation.
+    #[derive(thiserror::Error, Debug, Clone)]
+    pub enum Error {
+        // infallibe
+    }
+}
+
+impl TryFromVcf for PopulationFrequencies {
+    type Error = population_frequencies::Error;
+
+    fn try_from_vcf(
+        record: &vcf::variant::RecordBuf,
+        _header: &vcf::Header,
+    ) -> Result<Self, Self::Error> {
+        use vcf::variant::record_buf::info::field::Value;
+
+        macro_rules! extract_key {
+            ($key:ident) => {
+                let $key =
+                    if let Some(Some(Value::Integer($key))) = record.info().get(stringify!($key)) {
+                        *$key
+                    } else {
+                        0
+                    };
+            };
+        }
+
+        extract_key!(gnomad_exomes_an);
+        extract_key!(gnomad_exomes_hom);
+        extract_key!(gnomad_exomes_het);
+        extract_key!(gnomad_exomes_hemi);
+
+        extract_key!(gnomad_genomes_an);
+        extract_key!(gnomad_genomes_hom);
+        extract_key!(gnomad_genomes_het);
+        extract_key!(gnomad_genomes_hemi);
+
+        extract_key!(gnomad_mtdna_an);
+        extract_key!(gnomad_mtdna_hom);
+        extract_key!(gnomad_mtdna_het);
+
+        extract_key!(helix_an);
+        extract_key!(helix_hom);
+        extract_key!(helix_het);
+
+        Ok(PopulationFrequencies {
+            gnomad_exomes: NuclearFrequencies {
+                an: gnomad_exomes_an,
+                hom: gnomad_exomes_hom,
+                het: gnomad_exomes_het,
+                hemi: gnomad_exomes_hemi,
+            },
+            gnomad_genomes: NuclearFrequencies {
+                an: gnomad_genomes_an,
+                hom: gnomad_genomes_hom,
+                het: gnomad_genomes_het,
+                hemi: gnomad_genomes_hemi,
+            },
+            gnomad_mt: MitochondrialFrequencies {
+                an: gnomad_mtdna_an,
+                hom: gnomad_mtdna_hom,
+                het: gnomad_mtdna_het,
+            },
+            helixmtdb: MitochondrialFrequencies {
+                an: helix_an,
+                hom: helix_hom,
+                het: helix_het,
+            },
+            inhouse: Default::default(),
+        })
+    }
+}
+
+/// Sequence variant representation VCF-style.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct VcfVariant {
+    /// Chromosome.
+    pub chrom: String,
+    /// Position.
+    pub pos: i32,
+    /// Reference allele.
+    pub ref_allele: String,
+    /// Alternate allele.
+    pub alt_allele: String,
+}
+
+impl Into<annonars::common::spdi::Var> for VcfVariant {
+    fn into(self) -> annonars::common::spdi::Var {
+        annonars::common::spdi::Var::new(
+            annonars::common::cli::canonicalize(&self.chrom),
+            self.pos,
+            self.ref_allele,
+            self.alt_allele,
+        )
+    }
+}
+
+/// Supporting code for `VcfVariant`.
+pub(crate) mod vcf_variant {
+    /// Error type for `FromVcf` implementation.
+    #[derive(thiserror::Error, Debug, Clone)]
+    pub enum Error {
+        #[error("Missing POS value")]
+        MissingVariantStart,
+        #[error("Missing ALT values")]
+        MissingAlternateBases,
+    }
+}
+
+impl TryFromVcf for VcfVariant {
+    type Error = vcf_variant::Error;
+
+    fn try_from_vcf(
+        record: &vcf::variant::RecordBuf,
+        header: &vcf::Header,
+    ) -> Result<Self, Self::Error> {
+        let chrom = record.reference_sequence_name().to_string();
+        let pos = usize::from(
+            record
+                .variant_start()
+                .ok_or(Self::Error::MissingVariantStart)?,
+        ) as i32;
+
+        let ref_allele = record.reference_bases().to_string();
+        let alt_allele = record
+            .alternate_bases()
+            .as_ref()
+            .iter()
+            .next()
+            .ok_or(Self::Error::MissingAlternateBases)?
+            .to_string();
+
+        Ok(Self {
+            chrom,
+            pos,
+            ref_allele,
+            alt_allele,
+        })
+    }
+}
+
+/// Helper type with mapping from sample name to `CallInfo`.
+#[derive(Debug, Clone, Default)]
+pub struct CallInfos {
+    /// Mapping from sample name to `CallInfo`.
+    pub call_infos: indexmap::IndexMap<String, CallInfo>,
+}
+
+/// Supporting code for `CallInfos`.
+pub(crate) mod call_infos {
+    use crate::common::GenotypeToStringError;
+
+    /// Error type for `FromVcf` implementation.
+    #[derive(thiserror::Error, Debug, Clone)]
+    pub enum Error {
+        #[error("Empty FORMAT/AD")]
+        EmptyFormatAd,
+        #[error("Problem parsing genotype: {0}")]
+        GenotypeParseError(#[from] GenotypeToStringError),
+    }
+}
+
+impl TryFromVcf for CallInfos {
+    type Error = call_infos::Error;
+
+    fn try_from_vcf(
+        record: &vcf::variant::RecordBuf,
+        header: &vcf::Header,
+    ) -> Result<Self, Self::Error> {
+        use vcf::variant::record::samples::keys::key;
+        let mut result = indexmap::IndexMap::new();
+
+        for (name, sample) in header.sample_names().iter().zip(record.samples().values()) {
+            let genotype = if let Some(Some(
+                vcf::variant::record_buf::samples::sample::value::Value::Genotype(gt),
+            )) = sample.get(key::GENOTYPE)
+            {
+                Some(genotype_to_string(&gt)?)
+            } else {
+                None
+            };
+            let quality = if let Some(Some(
+                vcf::variant::record_buf::samples::sample::value::Value::Integer(quality),
+            )) = sample.get(key::CONDITIONAL_GENOTYPE_QUALITY)
+            {
+                Some(*quality as f32)
+            } else {
+                None
+            };
+            let dp = if let Some(Some(
+                vcf::variant::record_buf::samples::sample::value::Value::Integer(dp),
+            )) = sample.get(key::READ_DEPTH)
+            {
+                Some(*dp)
+            } else {
+                None
+            };
+            let ad =
+                if let Some(Some(vcf::variant::record_buf::samples::sample::value::Value::Array(
+                    vcf::variant::record_buf::samples::sample::value::Array::Integer(ad),
+                ))) = sample.get(key::READ_DEPTHS)
+                {
+                    Some(ad[1].ok_or(Self::Error::EmptyFormatAd)?)
+                } else {
+                    None
+                };
+            let phase_set = if let Some(Some(
+                vcf::variant::record_buf::samples::sample::value::Value::Integer(id),
+            )) = sample.get(key::PHASE_SET)
+            {
+                Some(*id)
+            } else {
+                None
+            };
+
+            result.insert(
+                name.clone(),
+                CallInfo {
+                    sample: name.clone(),
+                    genotype,
+                    quality,
+                    dp,
+                    ad,
+                    phasing_id: phase_set,
+                },
+            );
+        }
+
+        Ok(CallInfos { call_infos: result })
+    }
+}
+
+/// Helper type with `AnnField` records.
+#[derive(Debug, Clone, Default)]
+pub struct AnnFields {
+    /// Mapping from sample name to `CallInfo`.
+    pub ann_fields: Vec<mehari::annotate::seqvars::ann::AnnField>,
+}
+
+/// Supporting code for `AnnFields`.
+pub(crate) mod ann_fields {
+    /// Error type for `FromVcf` implementation.
+    #[derive(thiserror::Error, Debug, Clone)]
+    pub enum Error {
+        #[error("Problem parsing INFO/ANN: {0}")]
+        ParseError(String),
+        #[error("Invalid type of INFO/ANN")]
+        InvalidTypeInfoAnn,
+    }
+}
+
+impl TryFromVcf for AnnFields {
+    type Error = ann_fields::Error;
+
+    fn try_from_vcf(
+        record: &vcf::variant::RecordBuf,
+        _header: &vcf::Header,
+    ) -> Result<AnnFields, ann_fields::Error> {
+        if let Some(Some(ann)) = record.info().get("ANN") {
+            if let vcf::variant::record_buf::info::field::Value::Array(
+                vcf::variant::record_buf::info::field::value::Array::String(ann),
+            ) = ann
+            {
+                Ok(AnnFields {
+                    ann_fields: ann
+                        .iter()
+                        .flatten()
+                        .map(|s| s.parse::<mehari::annotate::seqvars::ann::AnnField>())
+                        .collect::<Result<Vec<_>, _>>()
+                        .map_err(|e| Self::Error::ParseError(format!("{}", e)))?,
+                })
+            } else {
+                return Err(ann_fields::Error::InvalidTypeInfoAnn);
+            }
+        } else {
+            Ok(Default::default())
+        }
+    }
+}
+
+/// Sequence variant record.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct VariantRecord {
+    /// VCF-style variant.
+    pub vcf_variant: VcfVariant,
+    /// Call information.
+    pub call_infos: indexmap::IndexMap<String, CallInfo>,
+    /// Annotation fields.
+    pub ann_fields: Vec<mehari::annotate::seqvars::ann::AnnField>,
+    /// Population frequencies.
+    pub population_frequencies: PopulationFrequencies,
+}
+
+/// Supporting code for `VariantRecord`.
+pub(crate) mod variant_record {
+    /// Error type for `FromVcf` implementation.
+    #[derive(thiserror::Error, Debug, Clone)]
+    pub enum Error {
+        #[error("Problem with variant description: {0:?}")]
+        VcfVariantError(#[from] super::vcf_variant::Error),
+        #[error("Problem with call information: {0:?}")]
+        CallInfosError(#[from] super::call_infos::Error),
+        #[error("Problem with annotation fields: {0:?}")]
+        AnnFieldsError(#[from] super::ann_fields::Error),
+        #[error("Problem with population frequencies: {0:?}")]
+        PopulationFrequenciesError(#[from] super::population_frequencies::Error),
+    }
+}
+
+impl TryFromVcf for VariantRecord {
+    type Error = variant_record::Error;
+
+    /// Convert from VCF record.
+    ///
+    /// # Arguments
+    ///
+    /// * `record` - VCF record.
+    /// * `header` - VCF header.
+    ///
+    /// # Errors
+    ///
+    /// Returns an error if the record cannot be extracted.
+    fn try_from_vcf(
+        record: &vcf::variant::RecordBuf,
+        header: &vcf::Header,
+    ) -> Result<Self, Self::Error> {
+        let vcf_variant = VcfVariant::try_from_vcf(record, header)?;
+        let CallInfos { call_infos } = CallInfos::try_from_vcf(record, header)?;
+        let AnnFields { ann_fields } = AnnFields::try_from_vcf(record, header)?;
+        let population_frequencies = PopulationFrequencies::try_from_vcf(record, header)?;
+
+        Ok(Self {
+            vcf_variant,
+            call_infos,
+            ann_fields,
+            population_frequencies,
+        })
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[rstest::fixture]
+    fn nuclear_frequencies() -> NuclearFrequencies {
+        NuclearFrequencies {
+            an: 100,
+            hom: 10,
+            het: 20,
+            hemi: 5,
+        }
+    }
+
+    #[rstest::fixture]
+    fn mitochondrial_frequencies() -> MitochondrialFrequencies {
+        MitochondrialFrequencies {
+            an: 100,
+            hom: 10,
+            het: 20,
+        }
+    }
+
+    #[rstest::fixture]
+    fn inhouse_frequencies() -> InHouseFrequencies {
+        InHouseFrequencies {
+            hom: 10,
+            het: 20,
+            hemi: 5,
+            total: 35,
+        }
+    }
+
+    #[rstest::fixture]
+    fn population_frequencies(
+        nuclear_frequencies: NuclearFrequencies,
+        mitochondrial_frequencies: MitochondrialFrequencies,
+        inhouse_frequencies: InHouseFrequencies,
+    ) -> PopulationFrequencies {
+        PopulationFrequencies {
+            gnomad_exomes: nuclear_frequencies.clone(),
+            gnomad_genomes: nuclear_frequencies.clone(),
+            gnomad_mt: mitochondrial_frequencies.clone(),
+            helixmtdb: mitochondrial_frequencies.clone(),
+            inhouse: inhouse_frequencies.clone(),
+        }
+    }
+
+    #[rstest::rstest]
+    fn test_nuclear_frequencies_an(nuclear_frequencies: NuclearFrequencies) {
+        assert_eq!(nuclear_frequencies.an(), 100);
+    }
+
+    #[rstest::rstest]
+    fn test_nuclear_frequencies_ac(nuclear_frequencies: NuclearFrequencies) {
+        assert_eq!(nuclear_frequencies.hom(), 10);
+        assert_eq!(nuclear_frequencies.het(), 20);
+        assert_eq!(nuclear_frequencies.ac(), 45);
+    }
+
+    #[rstest::rstest]
+    fn test_nuclear_frequencies_af(nuclear_frequencies: NuclearFrequencies) {
+        assert_eq!(nuclear_frequencies.af(), 0.45);
+    }
+
+    #[rstest::rstest]
+    fn test_nuclear_frequencies_hemi(nuclear_frequencies: NuclearFrequencies) {
+        assert_eq!(nuclear_frequencies.hemi(), 5);
+    }
+
+    #[rstest::rstest]
+    fn test_nuclear_frequencies_carriers(nuclear_frequencies: NuclearFrequencies) {
+        assert_eq!(nuclear_frequencies.carriers(), 35);
+    }
+
+    #[rstest::rstest]
+    fn test_mitochondrial_frequencies_an(mitochondrial_frequencies: MitochondrialFrequencies) {
+        assert_eq!(mitochondrial_frequencies.an(), 100);
+    }
+
+    #[rstest::rstest]
+    fn test_mitochondrial_frequencies_ac(mitochondrial_frequencies: MitochondrialFrequencies) {
+        assert_eq!(mitochondrial_frequencies.hom(), 10);
+        assert_eq!(mitochondrial_frequencies.het(), 20);
+        assert_eq!(mitochondrial_frequencies.ac(), 30);
+    }
+
+    #[rstest::rstest]
+    fn test_mitochondrial_frequencies_af(mitochondrial_frequencies: MitochondrialFrequencies) {
+        assert_eq!(mitochondrial_frequencies.af(), 0.3);
+    }
+
+    #[rstest::rstest]
+    fn test_mitochondrial_frequencies_carriers(
+        mitochondrial_frequencies: MitochondrialFrequencies,
+    ) {
+        assert_eq!(mitochondrial_frequencies.carriers(), 30);
+    }
+
+    #[rstest::rstest]
+    fn test_inhouse_frequencies_ac(inhouse_frequencies: InHouseFrequencies) {
+        assert_eq!(inhouse_frequencies.hom(), 10);
+        assert_eq!(inhouse_frequencies.het(), 20);
+        assert_eq!(inhouse_frequencies.ac(), 45);
+    }
+
+    #[rstest::rstest]
+    fn test_inhouse_frequencies_carriers(inhouse_frequencies: InHouseFrequencies) {
+        assert_eq!(inhouse_frequencies.carriers(), 35);
+    }
+
+    #[rstest::rstest]
+    fn test_population_frequencies(population_frequencies: PopulationFrequencies) {
+        assert_eq!(population_frequencies.gnomad_exomes.an, 100);
+        assert_eq!(population_frequencies.gnomad_genomes.an, 100);
+        assert_eq!(population_frequencies.gnomad_mt.an, 100);
+        assert_eq!(population_frequencies.helixmtdb.an, 100);
+        assert_eq!(population_frequencies.inhouse.total, 35);
+    }
+
+    #[rstest::rstest]
+    #[case("tests/seqvars/query/Case_1.ingested.vcf")]
+    #[case("tests/seqvars/query/dragen.ingested.vcf")]
+    pub fn sequence_variant_from_vcf(#[case] path_input: &str) -> Result<(), anyhow::Error> {
+        use noodles::vcf::variant::RecordBuf;
+
+        mehari::common::set_snapshot_suffix!("{}", path_input.split('/').last().unwrap());
+
+        let mut vcf_reader = vcf::io::reader::Builder::default()
+            .build_from_path(path_input)
+            .unwrap();
+        let header = vcf_reader.read_header()?;
+
+        for record in vcf_reader.records() {
+            let record = record?;
+            let seqvar = super::VariantRecord::try_from_vcf(
+                &RecordBuf::try_from_variant_record(&header, &record)?,
+                &header,
+            )?;
+
+            insta::assert_yaml_snapshot!(&seqvar);
+        }
+
+        Ok(())
+    }
+}
diff --git a/src/seqvars/query/schema/mod.rs b/src/seqvars/query/schema/mod.rs
new file mode 100644
index 00000000..2424e2b5
--- /dev/null
+++ b/src/seqvars/query/schema/mod.rs
@@ -0,0 +1,4 @@
+//! Internal Rust representations for query and data.
+
+pub mod data;
+pub mod query;
diff --git a/src/seqvars/query/schema/query.rs b/src/seqvars/query/schema/query.rs
new file mode 100644
index 00000000..065ddce3
--- /dev/null
+++ b/src/seqvars/query/schema/query.rs
@@ -0,0 +1,2197 @@
+//! Code for representing query definitions.
+//!
+//! We generally use protobuf JSON for representing queries when stored.
+//! After deserialization, they are converted into the data structures defined
+//! here.
+
+use crate::pbs::varfish::v1::seqvars::query as pb_query;
+
+/// Enumeration for recessvive mode queries.
+#[derive(
+    Debug,
+    Clone,
+    Copy,
+    Default,
+    PartialEq,
+    Eq,
+    PartialOrd,
+    Ord,
+    Hash,
+    serde::Serialize,
+    serde::Deserialize,
+)]
+pub enum RecessiveMode {
+    /// Disabled recessive mode,
+    #[default]
+    Disabled,
+    /// Compound heterozygous recessive mode.
+    CompoundHeterozygous,
+    /// Homozygous recessive mode.
+    Homozygous,
+    /// Generic recessive mode.
+    Any,
+}
+
+/// Supporting code for `RecessiveMode`.
+pub(crate) mod recessive_mode {
+    /// Error type for `RecessiveMode::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Cannot convert protobuf RecessiveMode: {0:?}")]
+        UnknownRecessiveModeValue(super::pb_query::RecessiveMode),
+    }
+}
+
+impl TryFrom<pb_query::RecessiveMode> for RecessiveMode {
+    type Error = recessive_mode::Error;
+
+    fn try_from(value: pb_query::RecessiveMode) -> Result<Self, Self::Error> {
+        match value {
+            pb_query::RecessiveMode::Disabled => Ok(RecessiveMode::Disabled),
+            pb_query::RecessiveMode::CompoundHeterozygous => {
+                Ok(RecessiveMode::CompoundHeterozygous)
+            }
+            pb_query::RecessiveMode::Homozygous => Ok(RecessiveMode::Homozygous),
+            pb_query::RecessiveMode::Any => Ok(RecessiveMode::Any),
+            _ => Err(recessive_mode::Error::UnknownRecessiveModeValue(value)),
+        }
+    }
+}
+
+/// Enumeration type for genotype choice.
+#[derive(
+    Debug,
+    Clone,
+    Copy,
+    Default,
+    PartialEq,
+    Eq,
+    PartialOrd,
+    Ord,
+    Hash,
+    serde::Serialize,
+    serde::Deserialize,
+)]
+pub enum GenotypeChoice {
+    /// Any genotype.
+    #[default]
+    Any,
+    /// Reference genotype.
+    Ref,
+    /// Heterozygous genotype.
+    Het,
+    /// Homozygous genotype.
+    Hom,
+    /// Non-heterozygous genotype.
+    NonHet,
+    /// Non-homozygous genotype.
+    NonHom,
+    /// Variant genotype.
+    Variant,
+    /// Recessive index.
+    RecessiveIndex,
+    /// Recessive parent.
+    RecessiveParent,
+}
+
+/// Supporting code for `GenotypeChoice`.
+pub(crate) mod genotype_choice {
+    /// Error type for `GenotypeChoice::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Cannot convert protobuf GenotypeChoice: {0:?}")]
+        UnknownGenotypeChoiceValue(super::pb_query::GenotypeChoice),
+    }
+}
+
+impl TryFrom<pb_query::GenotypeChoice> for GenotypeChoice {
+    type Error = genotype_choice::Error;
+
+    fn try_from(value: pb_query::GenotypeChoice) -> Result<Self, Self::Error> {
+        match value {
+            pb_query::GenotypeChoice::Any => Ok(GenotypeChoice::Any),
+            pb_query::GenotypeChoice::Ref => Ok(GenotypeChoice::Ref),
+            pb_query::GenotypeChoice::Het => Ok(GenotypeChoice::Het),
+            pb_query::GenotypeChoice::Hom => Ok(GenotypeChoice::Hom),
+            pb_query::GenotypeChoice::NonHet => Ok(GenotypeChoice::NonHet),
+            pb_query::GenotypeChoice::NonHom => Ok(GenotypeChoice::NonHom),
+            pb_query::GenotypeChoice::Variant => Ok(GenotypeChoice::Variant),
+            pb_query::GenotypeChoice::RecessiveIndex => Ok(GenotypeChoice::RecessiveIndex),
+            pb_query::GenotypeChoice::RecessiveParent => Ok(GenotypeChoice::RecessiveParent),
+            _ => Err(Self::Error::UnknownGenotypeChoiceValue(value)),
+        }
+    }
+}
+
+/// Trait that describes whether a string matches a value.
+///
+/// Note that we assume properly ingested VCFs with only one alternate allele.
+/// The valid genotype strings have the form "<VAL>/<VAL>", "<VAL>|<VAL>" or
+/// "<VAL>" with "<VAL>" being one of "0", "1", and ".".
+pub trait MatchesGenotypeStr {
+    /// Whether `self` matches `s`.
+    ///
+    /// # Arguments
+    ///
+    /// * `gt_str` - The string to match against.
+    ///
+    /// # Returns
+    ///
+    /// `true` if `self` matches `gt_str`, `false` otherwise.
+    fn matches(&self, gt_tr: &str) -> bool;
+}
+
+impl MatchesGenotypeStr for GenotypeChoice {
+    fn matches(&self, gt_str: &str) -> bool {
+        let gt_str = if gt_str.starts_with('/') || gt_str.starts_with('|') {
+            &gt_str[1..]
+        } else {
+            gt_str
+        };
+        match self {
+            GenotypeChoice::Any => true,
+            GenotypeChoice::Ref => ["0", "0|0", "0/0"].contains(&gt_str),
+            GenotypeChoice::RecessiveIndex
+            | GenotypeChoice::RecessiveParent
+            | GenotypeChoice::Het => ["0/1", "0|1", "1/0", "1|0"].contains(&gt_str),
+            GenotypeChoice::Hom => ["1", "1/1", "1|1"].contains(&gt_str),
+            GenotypeChoice::NonHom => !["1", "1/1", "1|1"].contains(&gt_str),
+            GenotypeChoice::NonHet => !["0/1", "0|1", "1/0", "1|0"].contains(&gt_str),
+            GenotypeChoice::Variant => {
+                ["1", "0/1", "0|1", "1/0", "1|0", "1|1", "1/1"].contains(&gt_str)
+            }
+        }
+    }
+}
+
+/// Query for a single sample.
+#[derive(Debug, Clone, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct SampleGenotypeChoice {
+    /// Name of the sample filtered for.
+    pub sample: String,
+    /// Genotype choice.
+    pub genotype: GenotypeChoice,
+    /// Whether to include no-call (will disable quality filter).
+    pub include_no_call: bool,
+    /// Whether to enable sample in filtration.
+    pub enabled: bool,
+}
+
+impl Default for SampleGenotypeChoice {
+    fn default() -> Self {
+        Self {
+            sample: Default::default(),
+            genotype: Default::default(),
+            include_no_call: false,
+            enabled: true,
+        }
+    }
+}
+
+/// Supporting code for `SampleGenotypeChoice`.
+pub(crate) mod sample_genotype_choice {
+    /// Error type for `SampleGenotypeChoice::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Cannot convert i32 into protobuf GenotypeChoice: {0}")]
+        UnknownGenotypeChoiceInt(i32),
+        #[error("Cannot convert protobuf GenotypeChoice: {0:?}")]
+        UnknownGenotypeChoiceValue(super::pb_query::GenotypeChoice),
+    }
+}
+
+impl TryFrom<pb_query::SampleGenotypeChoice> for SampleGenotypeChoice {
+    type Error = sample_genotype_choice::Error;
+
+    fn try_from(value: pb_query::SampleGenotypeChoice) -> Result<Self, Self::Error> {
+        let pb_genotype = pb_query::GenotypeChoice::try_from(value.genotype)
+            .map_err(|_| Self::Error::UnknownGenotypeChoiceInt(value.genotype))?;
+        Ok(Self {
+            sample: value.sample,
+            genotype: GenotypeChoice::try_from(pb_genotype)
+                .map_err(|_| Self::Error::UnknownGenotypeChoiceValue(pb_genotype))?,
+            include_no_call: value.include_no_call,
+            enabled: value.enabled,
+        })
+    }
+}
+
+/// Query settings for genotypes.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct QuerySettingsGenotype {
+    /// Recessive mode.
+    pub recessive_mode: RecessiveMode,
+    /// Mapping from sample name to sample genotype choice.
+    pub sample_genotypes: indexmap::IndexMap<String, SampleGenotypeChoice>,
+}
+
+/// Support code for `QuerySettingsGenotype`.
+pub(crate) mod query_settings_genotype {
+    /// Error type for `QuerySettingsGenotype::recessive_index()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum RecessiveIndexError {
+        #[error("No recessive index sample found")]
+        NoRecessiveIndexSample,
+        #[error("Multiple recessive index samples found: {0:?}")]
+        MultipleRecessiveIndexSamples(Vec<String>),
+    }
+
+    /// Error type for `QuerySettingsGenotype::recessive_parents()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum RecessiveParentsError {
+        #[error("Too many recessive parent samples found: {0:?}")]
+        TooManyRecessiveParentsFound(Vec<String>),
+    }
+
+    /// Error type for `QuerySettingsGenotype::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Cannot convert i32 into protobuf RecessiveMode: {0}")]
+        UnknownRecessiveModeInt(i32),
+        #[error("Cannot convert protobuf RecessiveMode: {0:?}")]
+        UnknownRecessiveModeValue(super::pb_query::RecessiveMode),
+        #[error("Sample occured twice in sample_genotypes: {0:?}")]
+        DuplicateSample(String),
+        #[error("Invalid sample genotype choice: {0}")]
+        InvalidSampleGenotypeChoice(#[from] super::sample_genotype_choice::Error),
+    }
+}
+
+impl QuerySettingsGenotype {
+    /// Return the selected recessive index sample.
+    ///
+    /// # Returns
+    ///
+    /// The sample name of the recessive index sample.
+    ///
+    /// # Errors
+    ///
+    /// * `RecessiveIndexError::NoRecessiveIndexSample` if no recessive index sample is found.
+    /// * `RecessiveIndexError::MultipleRecessiveIndexSamples` if multiple recessive index samples are found.
+    pub fn recessive_index(&self) -> Result<String, query_settings_genotype::RecessiveIndexError> {
+        let samples = self
+            .sample_genotypes
+            .values()
+            .filter(|sgc| sgc.genotype == GenotypeChoice::RecessiveIndex)
+            .map(|sgc| sgc.sample.clone())
+            .collect::<Vec<_>>();
+        if samples.is_empty() {
+            Err(query_settings_genotype::RecessiveIndexError::NoRecessiveIndexSample)
+        } else if samples.len() > 1 {
+            Err(
+                query_settings_genotype::RecessiveIndexError::MultipleRecessiveIndexSamples(
+                    samples,
+                ),
+            )
+        } else {
+            Ok(samples[0].clone())
+        }
+    }
+
+    /// Return the selected recessive parent samples.
+    ///
+    /// # Returns
+    ///
+    /// The sample names of the recessive parent samples (zero to two).
+    ///
+    /// # Errors
+    ///
+    /// * `RecessiveParentsError::TooManyRecessiveParentsFound` if more than two recessive parent samples are found.
+    pub fn recessive_parents(
+        &self,
+    ) -> Result<Vec<String>, query_settings_genotype::RecessiveParentsError> {
+        let samples = self
+            .sample_genotypes
+            .values()
+            .filter(|sgc| sgc.genotype == GenotypeChoice::RecessiveParent)
+            .map(|sgc| sgc.sample.clone())
+            .collect::<Vec<_>>();
+        if samples.len() > 2 {
+            Err(
+                query_settings_genotype::RecessiveParentsError::TooManyRecessiveParentsFound(
+                    samples,
+                ),
+            )
+        } else {
+            Ok(samples)
+        }
+    }
+}
+
+impl TryFrom<pb_query::QuerySettingsGenotype> for QuerySettingsGenotype {
+    type Error = query_settings_genotype::Error;
+
+    fn try_from(value: pb_query::QuerySettingsGenotype) -> Result<Self, Self::Error> {
+        let pb_recessive_mode = pb_query::RecessiveMode::try_from(value.recessive_mode)
+            .map_err(|_| Self::Error::UnknownRecessiveModeInt(value.recessive_mode))?;
+        let recessive_mode = RecessiveMode::try_from(pb_recessive_mode)
+            .map_err(|_| Self::Error::UnknownRecessiveModeValue(pb_recessive_mode))?;
+
+        let mut sample_genotypes = indexmap::IndexMap::new();
+        for pb_sample_genotype in value.sample_genotypes {
+            let sample_genotype = SampleGenotypeChoice::try_from(pb_sample_genotype)
+                .map_err(|e| Self::Error::InvalidSampleGenotypeChoice(e))?;
+            if sample_genotypes.contains_key(&sample_genotype.sample) {
+                return Err(Self::Error::DuplicateSample(sample_genotype.sample));
+            }
+            sample_genotypes.insert(sample_genotype.sample.clone(), sample_genotype);
+        }
+
+        Ok(Self {
+            recessive_mode,
+            sample_genotypes,
+        })
+    }
+}
+
+/// Quality settings for one sample.
+#[derive(Debug, Clone, Default, PartialEq, serde::Serialize, serde::Deserialize)]
+pub struct SampleQualitySettings {
+    /// Name of the sample filtered for.
+    pub sample: String,
+    /// Drop whole variant on failure.
+    pub filter_active: bool,
+    /// Minimal coverage for het. sites.
+    pub min_dp_het: Option<i32>,
+    /// Minimal coverage for hom. sites.
+    pub min_dp_hom: Option<i32>,
+    /// Minimal genotype quality.
+    pub min_gq: Option<i32>,
+    /// Minimal allele balance for het. variants.
+    pub min_ab: Option<f32>,
+    /// Minimal number of alternate reads.
+    pub min_ad: Option<i32>,
+    /// Maximal number of alternate reads.
+    pub max_ad: Option<i32>,
+}
+
+impl Eq for SampleQualitySettings {}
+
+impl From<pb_query::SampleQualitySettings> for SampleQualitySettings {
+    fn from(value: pb_query::SampleQualitySettings) -> Self {
+        Self {
+            sample: value.sample,
+            filter_active: value.filter_active,
+            min_dp_het: value.min_dp_het,
+            min_dp_hom: value.min_dp_hom,
+            min_gq: value.min_gq,
+            min_ab: value.min_ab,
+            min_ad: value.min_ad,
+            max_ad: value.max_ad,
+        }
+    }
+}
+
+/// Per-sample quality filter settings.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct QuerySettingsQuality {
+    /// Mapping from sample name to sample quality settings.
+    pub sample_qualities: indexmap::IndexMap<String, SampleQualitySettings>,
+}
+
+/// Supporting code for `QuerySettingsQuality`.
+pub(crate) mod query_settings_quality {
+    /// Error type for `QuerySettingsQuality::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Sample occured twice in sample_qualities: {0:?}")]
+        DuplicateSample(String),
+    }
+}
+
+impl TryFrom<pb_query::QuerySettingsQuality> for QuerySettingsQuality {
+    type Error = query_settings_quality::Error;
+
+    fn try_from(value: pb_query::QuerySettingsQuality) -> Result<Self, Self::Error> {
+        let mut sample_qualities = indexmap::IndexMap::new();
+        for pb_sample_quality in value.sample_qualities {
+            let sample_quality = SampleQualitySettings::from(pb_sample_quality);
+            if sample_qualities.contains_key(&sample_quality.sample) {
+                return Err(Self::Error::DuplicateSample(sample_quality.sample));
+            }
+            sample_qualities.insert(sample_quality.sample.clone(), sample_quality);
+        }
+        Ok(Self { sample_qualities })
+    }
+}
+
+/// gnomAD nuclear filter options.
+#[derive(Debug, Clone, Default, PartialEq, serde::Serialize, serde::Deserialize)]
+pub struct GnomadNuclearFrequencySettings {
+    /// Whether to enable filtration by 1000 Genomes.
+    pub enabled: bool,
+    /// Maximal number of in-house heterozygous carriers.
+    pub heterozygous: Option<i32>,
+    /// Maximal number of in-house homozygous carriers.
+    pub homozygous: Option<i32>,
+    /// Maximal number of in-house hemizygous carriers.
+    pub hemizygous: Option<i32>,
+    /// Maximal allele frequency.
+    pub frequency: Option<f32>,
+}
+
+impl Eq for GnomadNuclearFrequencySettings {}
+
+impl From<pb_query::GnomadNuclearFreqyencySettings> for GnomadNuclearFrequencySettings {
+    fn from(value: pb_query::GnomadNuclearFreqyencySettings) -> Self {
+        Self {
+            enabled: value.enabled,
+            heterozygous: value.heterozygous,
+            homozygous: value.homozygous,
+            hemizygous: value.hemizygous,
+            frequency: value.frequency,
+        }
+    }
+}
+
+/// gnomAD mitochondrial filter options.
+#[derive(Debug, Clone, Default, PartialEq, serde::Serialize, serde::Deserialize)]
+pub struct GnomadMitochondrialFrequencySettings {
+    /// Whether to enable filtration by 1000 Genomes.
+    pub enabled: bool,
+    /// Maximal number of heteroplasmic carriers.
+    pub heteroplasmic: Option<i32>,
+    /// Maximal number of homoplasmic carriers.
+    pub homoplasmic: Option<i32>,
+    /// Maximal allele frequency.
+    pub frequency: Option<f32>,
+}
+
+impl Eq for GnomadMitochondrialFrequencySettings {}
+
+impl From<pb_query::GnomadMitochondrialFrequencySettings> for GnomadMitochondrialFrequencySettings {
+    fn from(value: pb_query::GnomadMitochondrialFrequencySettings) -> Self {
+        Self {
+            enabled: value.enabled,
+            heteroplasmic: value.heteroplasmic,
+            homoplasmic: value.homoplasmic,
+            frequency: value.frequency,
+        }
+    }
+}
+
+/// HelixMtDb filter options.
+#[derive(Debug, Clone, Default, PartialEq, serde::Serialize, serde::Deserialize)]
+pub struct HelixMtDbFrequencySettings {
+    /// Whether to enable filtration by mtDB.
+    pub enabled: bool,
+    /// Maximal number of heterozygous carriers in HelixMtDb.
+    pub heteroplasmic: Option<i32>,
+    /// Maximal number of homozygous carriers in HelixMtDb.
+    pub homoplasmic: Option<i32>,
+    /// Maximal frequency in HelixMtDb.
+    pub frequency: Option<f32>,
+}
+
+impl Eq for HelixMtDbFrequencySettings {}
+
+impl From<pb_query::HelixMtDbFrequencySettings> for HelixMtDbFrequencySettings {
+    fn from(value: pb_query::HelixMtDbFrequencySettings) -> Self {
+        Self {
+            enabled: value.enabled,
+            heteroplasmic: value.heteroplasmic,
+            homoplasmic: value.homoplasmic,
+            frequency: value.frequency,
+        }
+    }
+}
+
+/// In-house frequency filter options.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct InhouseFrequencySettings {
+    /// Whether to enable filtration by 1000 Genomes.
+    pub enabled: bool,
+    /// Maximal number of in-house heterozygous carriers.
+    pub heterozygous: Option<i32>,
+    /// Maximal number of in-house homozygous carriers.
+    pub homozygous: Option<i32>,
+    /// Maximal number of in-house hemizygous carriers.
+    pub hemizygous: Option<i32>,
+    /// Maximal number of in-house carriers.
+    pub carriers: Option<i32>,
+}
+
+impl From<pb_query::InhouseFrequencySettings> for InhouseFrequencySettings {
+    fn from(value: pb_query::InhouseFrequencySettings) -> Self {
+        Self {
+            enabled: value.enabled,
+            heterozygous: value.heterozygous,
+            homozygous: value.homozygous,
+            hemizygous: value.hemizygous,
+            carriers: value.carriers,
+        }
+    }
+}
+
+/// Query settings for population frequencies.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct QuerySettingsFrequency {
+    /// gnomAD-exomes filter.
+    pub gnomad_exomes: GnomadNuclearFrequencySettings,
+    /// gnomAD-genomes filter.
+    pub gnomad_genomes: GnomadNuclearFrequencySettings,
+    /// gnomAD-MT filter.
+    pub gnomad_mt: GnomadMitochondrialFrequencySettings,
+    /// HelixMtDb filter.
+    pub helixmtdb: HelixMtDbFrequencySettings,
+    /// In-house filter.
+    pub inhouse: InhouseFrequencySettings,
+}
+
+/// Supporting code for `QuerySettingsFrequency`.
+pub(crate) mod query_settings_frequency {
+    /// Error type for `QuerySettingsFrequency::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("gnomad_exomes missing in protobuf")]
+        GnomadExomesMissing,
+        #[error("gnomad_genomes missing in protobuf")]
+        GnomadGenomesMissing,
+        #[error("gnomad_mt missing in protobuf")]
+        GnomadMtMissing,
+        #[error("helixmtdb missing in protobuf")]
+        HelixMtDbMissing,
+        #[error("inhouse missing in protobuf")]
+        InhouseMissing,
+    }
+}
+
+impl TryFrom<pb_query::QuerySettingsFrequency> for QuerySettingsFrequency {
+    type Error = query_settings_frequency::Error;
+
+    fn try_from(value: pb_query::QuerySettingsFrequency) -> Result<Self, Self::Error> {
+        Ok(Self {
+            gnomad_exomes: GnomadNuclearFrequencySettings::from(
+                value
+                    .gnomad_exomes
+                    .ok_or(Self::Error::GnomadExomesMissing)?,
+            ),
+            gnomad_genomes: GnomadNuclearFrequencySettings::from(
+                value
+                    .gnomad_genomes
+                    .ok_or(Self::Error::GnomadGenomesMissing)?,
+            ),
+            gnomad_mt: GnomadMitochondrialFrequencySettings::from(
+                value.gnomad_mt.ok_or(Self::Error::GnomadMtMissing)?,
+            ),
+            helixmtdb: HelixMtDbFrequencySettings::from(
+                value.helixmtdb.ok_or(Self::Error::HelixMtDbMissing)?,
+            ),
+            inhouse: InhouseFrequencySettings::from(
+                value.inhouse.ok_or(Self::Error::InhouseMissing)?,
+            ),
+        })
+    }
+}
+
+/// Variant Types.
+#[derive(
+    Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, serde::Serialize, serde::Deserialize,
+)]
+pub enum VariantType {
+    /// SNV.
+    Snv,
+    /// Indel.
+    Indel,
+    /// MNV.
+    Mnv,
+    /// Complex substitution.
+    ComplexSubstitution,
+}
+
+/// Supporting code for `VariantType`.
+pub(crate) mod variant_type {
+    /// Error type for `VariantType::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Cannot convert protobuf VariantType: {0:?}")]
+        UnknownVariantTypeValue(super::pb_query::VariantType),
+    }
+}
+
+impl TryFrom<pb_query::VariantType> for VariantType {
+    type Error = variant_type::Error;
+
+    fn try_from(value: pb_query::VariantType) -> Result<Self, Self::Error> {
+        match value {
+            pb_query::VariantType::Snv => Ok(VariantType::Snv),
+            pb_query::VariantType::Indel => Ok(VariantType::Indel),
+            pb_query::VariantType::Mnv => Ok(VariantType::Mnv),
+            pb_query::VariantType::ComplexSubstitution => Ok(VariantType::ComplexSubstitution),
+            _ => Err(variant_type::Error::UnknownVariantTypeValue(value)),
+        }
+    }
+}
+
+/// Transcript types.
+#[derive(
+    Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, serde::Serialize, serde::Deserialize,
+)]
+pub enum TranscriptType {
+    /// Coding transcripts.
+    Coding,
+    /// Non-coding transcripts.
+    NonCoding,
+}
+
+/// Supporting code for `TranscriptType`.
+pub(crate) mod transcript_type {
+    /// Error type for `TranscriptType::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Cannot convert protobuf TranscriptType: {0:?}")]
+        UnknownTranscriptTypeValue(super::pb_query::TranscriptType),
+    }
+}
+
+impl TryFrom<pb_query::TranscriptType> for TranscriptType {
+    type Error = transcript_type::Error;
+
+    fn try_from(value: pb_query::TranscriptType) -> Result<Self, Self::Error> {
+        match value {
+            pb_query::TranscriptType::Coding => Ok(TranscriptType::Coding),
+            pb_query::TranscriptType::NonCoding => Ok(TranscriptType::NonCoding),
+            _ => Err(transcript_type::Error::UnknownTranscriptTypeValue(value)),
+        }
+    }
+}
+
+/// Consequence types.
+#[derive(
+    Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash, serde::Serialize, serde::Deserialize, strum::EnumIter
+)]
+pub enum Consequence {
+    /*
+     * High impact.
+     */
+    /// Transcript ablation.
+    TranscriptAblation,
+    /// Exon loss variant.
+    ExonLossVariant,
+    /// Splice acceptor variant.
+    SpliceAcceptorVariant,
+    /// Splice donor variant.
+    SpliceDonorVariant,
+    /// Stop gained.
+    StopGained,
+    /// Frameshift variant.
+    FrameshiftVariant,
+    /// Stop lost.
+    StopLost,
+    /// Start lost.
+    StartLost,
+    /// Transcript amplification.
+    TranscriptAmplification,
+    /*
+     * Moderate impact.
+     */
+    /// Disruptive inframe insertion.
+    DisruptiveInframeInsertion,
+    /// Disruptive inframe deletion.
+    DisruptiveInframeDeletion,
+    /// Conservative inframe insertion.
+    ConservativeInframeInsertion,
+    /// Conservative inframe deletion.
+    ConservativeInframeDeletion,
+    /// Missense variant.
+    MissenseVariant,
+    /*
+     * Low impact.
+     */
+    /// Splice donor 5th base variant.
+    SpliceDonorFifthBaseVariant,
+    /// Splice region variant.
+    SpliceRegionVariant,
+    /// Splice donor region variant.
+    SpliceDonorRegionVariant,
+    /// Splice polypyrimidine tract variant.
+    SplicePolypyrimidineTractVariant,
+    /// Start retained variant.
+    StartRetainedVariant,
+    /// Stop retained variant.
+    StopRetainedVariant,
+    /// Synonymous variant.
+    SynonymousVariant,
+    /*
+     * Modifier.
+     */
+    /// Coding sequence variant.
+    CodingSequenceVariant,
+    /// 5' UTR exon variant.
+    FivePrimeUtrExonVariant,
+    /// 5' UTR intron variant.
+    FivePrimeUtrIntronVariant,
+    /// 3' UTR exon variant.
+    ThreePrimeUtrExonVariant,
+    /// 3' UTR intron variant.
+    ThreePrimeUtrIntronVariant,
+    /// Non-coding transcript exon variant.
+    NonCodingTranscriptExonVariant,
+    /// Non-coding transcript intron variant.
+    NonCodingTranscriptIntronVariant,
+    /// Upstream gene variant.
+    UpstreamGeneVariant,
+    /// Downstream gene variant.
+    DownstreamGeneVariant,
+    /// Intergenic variant.
+    IntergenicVariant,
+    /// Intron variant.
+    IntronVariant,
+}
+
+/// Supporting code for `Consequence`.
+pub(crate) mod consequence {
+    /// Error type for `Consequence::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Cannot convert protobuf Consequence: {0:?}")]
+        UnknownConsequenceValue(super::pb_query::Consequence),
+    }
+}
+
+impl TryFrom<pb_query::Consequence> for Consequence {
+    type Error = consequence::Error;
+
+    fn try_from(value: pb_query::Consequence) -> Result<Self, Self::Error> {
+        match value {
+            pb_query::Consequence::TranscriptAblation => Ok(Consequence::TranscriptAblation),
+            pb_query::Consequence::ExonLossVariant => Ok(Consequence::ExonLossVariant),
+            pb_query::Consequence::SpliceAcceptorVariant => Ok(Consequence::SpliceAcceptorVariant),
+            pb_query::Consequence::SpliceDonorVariant => Ok(Consequence::SpliceDonorVariant),
+            pb_query::Consequence::StopGained => Ok(Consequence::StopGained),
+            pb_query::Consequence::FrameshiftVariant => Ok(Consequence::FrameshiftVariant),
+            pb_query::Consequence::StopLost => Ok(Consequence::StopLost),
+            pb_query::Consequence::StartLost => Ok(Consequence::StartLost),
+            pb_query::Consequence::TranscriptAmplification => {
+                Ok(Consequence::TranscriptAmplification)
+            }
+            pb_query::Consequence::DisruptiveInframeInsertion => {
+                Ok(Consequence::DisruptiveInframeInsertion)
+            }
+            pb_query::Consequence::DisruptiveInframeDeletion => {
+                Ok(Consequence::DisruptiveInframeDeletion)
+            }
+            pb_query::Consequence::ConservativeInframeInsertion => {
+                Ok(Consequence::ConservativeInframeInsertion)
+            }
+            pb_query::Consequence::ConservativeInframeDeletion => {
+                Ok(Consequence::ConservativeInframeDeletion)
+            }
+            pb_query::Consequence::MissenseVariant => Ok(Consequence::MissenseVariant),
+            pb_query::Consequence::SpliceDonorFifthBaseVariant => {
+                Ok(Consequence::SpliceDonorFifthBaseVariant)
+            }
+            pb_query::Consequence::SpliceRegionVariant => Ok(Consequence::SpliceRegionVariant),
+            pb_query::Consequence::SpliceDonorRegionVariant => {
+                Ok(Consequence::SpliceDonorRegionVariant)
+            }
+            pb_query::Consequence::SplicePolypyrimidineTractVariant => {
+                Ok(Consequence::SplicePolypyrimidineTractVariant)
+            }
+            pb_query::Consequence::StartRetainedVariant => Ok(Consequence::StartRetainedVariant),
+            pb_query::Consequence::StopRetainedVariant => Ok(Consequence::StopRetainedVariant),
+            pb_query::Consequence::SynonymousVariant => Ok(Consequence::SynonymousVariant),
+            pb_query::Consequence::CodingSequenceVariant => Ok(Consequence::CodingSequenceVariant),
+            pb_query::Consequence::FivePrimeUtrExonVariant => {
+                Ok(Consequence::FivePrimeUtrExonVariant)
+            }
+            pb_query::Consequence::FivePrimeUtrIntronVariant => {
+                Ok(Consequence::FivePrimeUtrIntronVariant)
+            }
+            pb_query::Consequence::ThreePrimeUtrExonVariant => {
+                Ok(Consequence::ThreePrimeUtrExonVariant)
+            }
+            pb_query::Consequence::ThreePrimeUtrIntronVariant => {
+                Ok(Consequence::ThreePrimeUtrIntronVariant)
+            }
+            pb_query::Consequence::NonCodingTranscriptExonVariant => {
+                Ok(Consequence::NonCodingTranscriptExonVariant)
+            }
+            pb_query::Consequence::NonCodingTranscriptIntronVariant => {
+                Ok(Consequence::NonCodingTranscriptIntronVariant)
+            }
+            pb_query::Consequence::UpstreamGeneVariant => Ok(Consequence::UpstreamGeneVariant),
+            pb_query::Consequence::DownstreamGeneVariant => Ok(Consequence::DownstreamGeneVariant),
+            pb_query::Consequence::IntergenicVariant => Ok(Consequence::IntergenicVariant),
+            pb_query::Consequence::IntronVariant => Ok(Consequence::IntronVariant),
+            _ => Err(consequence::Error::UnknownConsequenceValue(value)),
+        }
+    }
+}
+
+impl Into<mehari::annotate::seqvars::ann::Consequence> for Consequence {
+    fn into(self) -> mehari::annotate::seqvars::ann::Consequence {
+        use mehari::annotate::seqvars::ann;
+
+        match self {
+            Consequence::TranscriptAblation => ann::Consequence::TranscriptAblation,
+            Consequence::ExonLossVariant => ann::Consequence::ExonLossVariant,
+            Consequence::SpliceAcceptorVariant => ann::Consequence::SpliceAcceptorVariant,
+            Consequence::SpliceDonorVariant => ann::Consequence::SpliceDonorVariant,
+            Consequence::StopGained => ann::Consequence::StopGained,
+            Consequence::FrameshiftVariant => ann::Consequence::FrameshiftVariant,
+            Consequence::StopLost => ann::Consequence::StopLost,
+            Consequence::StartLost => ann::Consequence::StartLost,
+            Consequence::TranscriptAmplification => ann::Consequence::TranscriptAmplification,
+            Consequence::DisruptiveInframeInsertion => ann::Consequence::DisruptiveInframeInsertion,
+            Consequence::DisruptiveInframeDeletion => ann::Consequence::DisruptiveInframeDeletion,
+            Consequence::ConservativeInframeInsertion => {
+                ann::Consequence::ConservativeInframeInsertion
+            }
+            Consequence::ConservativeInframeDeletion => {
+                ann::Consequence::ConservativeInframeDeletion
+            }
+            Consequence::MissenseVariant => ann::Consequence::MissenseVariant,
+            Consequence::SpliceDonorFifthBaseVariant => {
+                ann::Consequence::SpliceDonorFifthBaseVariant
+            }
+            Consequence::SpliceRegionVariant => ann::Consequence::SpliceRegionVariant,
+            Consequence::SpliceDonorRegionVariant => ann::Consequence::SpliceDonorRegionVariant,
+            Consequence::SplicePolypyrimidineTractVariant => {
+                ann::Consequence::SplicePolypyrimidineTractVariant
+            }
+            Consequence::StartRetainedVariant => ann::Consequence::StartRetainedVariant,
+            Consequence::StopRetainedVariant => ann::Consequence::StopRetainedVariant,
+            Consequence::SynonymousVariant => ann::Consequence::SynonymousVariant,
+            Consequence::CodingSequenceVariant => ann::Consequence::CodingSequenceVariant,
+            Consequence::FivePrimeUtrExonVariant => ann::Consequence::FivePrimeUtrExonVariant,
+            Consequence::FivePrimeUtrIntronVariant => ann::Consequence::FivePrimeUtrIntronVariant,
+            Consequence::ThreePrimeUtrExonVariant => ann::Consequence::ThreePrimeUtrExonVariant,
+            Consequence::ThreePrimeUtrIntronVariant => ann::Consequence::ThreePrimeUtrIntronVariant,
+            Consequence::NonCodingTranscriptExonVariant => {
+                ann::Consequence::NonCodingTranscriptExonVariant
+            }
+            Consequence::NonCodingTranscriptIntronVariant => {
+                ann::Consequence::NonCodingTranscriptIntronVariant
+            }
+            Consequence::UpstreamGeneVariant => ann::Consequence::UpstreamGeneVariant,
+            Consequence::DownstreamGeneVariant => ann::Consequence::DownstreamGeneVariant,
+            Consequence::IntergenicVariant => ann::Consequence::IntergenicVariant,
+            Consequence::IntronVariant => ann::Consequence::IntronVariant,
+        }
+    }
+}
+
+/// Query settings for consequence types.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct QuerySettingsConsequence {
+    /// Variant types.
+    pub variant_types: Vec<VariantType>,
+    /// Transcript types.
+    pub transcript_types: Vec<TranscriptType>,
+    /// Consequences to consider.
+    pub consequences: Vec<Consequence>,
+    /// Maximal distance to next exon.
+    pub max_dist_to_exon: Option<i32>,
+}
+
+/// Supporting code for `QuerySettingsConsequence`.
+pub(crate) mod query_settings_consequence {
+    /// Error type for `QuerySettingsConsequence::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Cannot convert i32 into protobuf VariantType: {0}")]
+        UnknownVariantTypeInt(i32),
+        #[error("Cannot convert protobuf VariantType: {0:?}")]
+        UnknownVariantTypeValue(super::pb_query::VariantType),
+        #[error("Cannot convert i32 into protobuf TranscriptType: {0}")]
+        UnknownTranscriptTypeInt(i32),
+        #[error("Cannot convert protobuf TranscriptType: {0:?}")]
+        UnknownTranscriptTypeValue(super::pb_query::TranscriptType),
+        #[error("Cannot convert i32 into protobuf Consequence: {0}")]
+        UnknownConsequenceInt(i32),
+        #[error("Cannot convert protobuf Consequence: {0:?}")]
+        UnknownConsequenceValue(super::pb_query::Consequence),
+    }
+}
+
+impl TryFrom<pb_query::QuerySettingsConsequence> for QuerySettingsConsequence {
+    type Error = query_settings_consequence::Error;
+
+    fn try_from(value: pb_query::QuerySettingsConsequence) -> Result<Self, Self::Error> {
+        let variant_types = value
+            .variant_types
+            .into_iter()
+            .map(|v| {
+                let v = pb_query::VariantType::try_from(v)
+                    .map_err(|_| query_settings_consequence::Error::UnknownVariantTypeInt(v))?;
+                VariantType::try_from(v)
+                    .map_err(|_| query_settings_consequence::Error::UnknownVariantTypeValue(v))
+            })
+            .collect::<Result<Vec<_>, _>>()?;
+        let transcript_types = value
+            .transcript_types
+            .into_iter()
+            .map(|v| {
+                let v = pb_query::TranscriptType::try_from(v)
+                    .map_err(|_| query_settings_consequence::Error::UnknownTranscriptTypeInt(v))?;
+                TranscriptType::try_from(v)
+                    .map_err(|_| query_settings_consequence::Error::UnknownTranscriptTypeValue(v))
+            })
+            .collect::<Result<Vec<_>, _>>()?;
+        let consequences = value
+            .consequences
+            .into_iter()
+            .map(|v| {
+                let v = pb_query::Consequence::try_from(v)
+                    .map_err(|_| query_settings_consequence::Error::UnknownConsequenceInt(v))?;
+                Consequence::try_from(v)
+                    .map_err(|_| query_settings_consequence::Error::UnknownConsequenceValue(v))
+            })
+            .collect::<Result<Vec<_>, _>>()?;
+        Ok(Self {
+            variant_types,
+            transcript_types,
+            consequences,
+            max_dist_to_exon: value.max_dist_to_exon,
+        })
+    }
+}
+
+/// A 1-based integer range.
+#[derive(Debug, Clone, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct Range {
+    /// 1-based start position.
+    pub start: i32,
+    /// 1-based end position.
+    pub end: i32,
+}
+
+impl From<pb_query::Range> for Range {
+    fn from(value: pb_query::Range) -> Self {
+        Self {
+            start: value.start,
+            end: value.end,
+        }
+    }
+}
+
+/// Genomic region.
+#[derive(Debug, Clone, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct GenomicRegion {
+    /// Chromosome.
+    pub chrom: String,
+    /// Range of region.
+    pub range: Option<Range>,
+}
+
+impl From<pb_query::GenomicRegion> for GenomicRegion {
+    fn from(value: pb_query::GenomicRegion) -> Self {
+        Self {
+            chrom: value.chrom,
+            range: value.range.map(Range::from),
+        }
+    }
+}
+
+/// Query settings for locus.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct QuerySettingsLocus {
+    /// List of HGNC identifiers for filtration to genes.
+    pub genes: Vec<String>,
+    /// List of genomic regions to limit restrict the resulting variants to.
+    pub genome_regions: Vec<GenomicRegion>,
+}
+
+impl From<pb_query::QuerySettingsLocus> for QuerySettingsLocus {
+    fn from(value: pb_query::QuerySettingsLocus) -> Self {
+        Self {
+            genes: value.genes,
+            genome_regions: value
+                .genome_regions
+                .into_iter()
+                .map(GenomicRegion::from)
+                .collect(),
+        }
+    }
+}
+
+// Canonical ClinVar germline aggregate descriptions.
+#[derive(Debug, Clone, Copy, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub enum ClinvarGermlineAggregateDescription {
+    /// Pathogenic.
+    Pathogenic,
+    /// Likely pathogenic.
+    LikelyPathogenic,
+    /// Uncertain significance.
+    UncertainSignificance,
+    /// Likely benign.
+    LikelyBenign,
+    /// Benign.
+    Benign,
+}
+
+/// Supporting code for `ClinvarGermlineAggregateDescription`.
+pub(crate) mod clinvar_germline_aggregate_description {
+    /// Error type for `ClinvarGermlineAggregateDescription::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Cannot convert protobuf ClinvarGermlineAggregateDescription: {0:?}")]
+        UnknownClinvarGermlineAggregateDescriptionValue(
+            super::pb_query::ClinvarGermlineAggregateDescription,
+        ),
+    }
+}
+
+impl TryFrom<pb_query::ClinvarGermlineAggregateDescription>
+    for ClinvarGermlineAggregateDescription
+{
+    type Error = clinvar_germline_aggregate_description::Error;
+
+    fn try_from(value: pb_query::ClinvarGermlineAggregateDescription) -> Result<Self, Self::Error> {
+        match value {
+            pb_query::ClinvarGermlineAggregateDescription::Pathogenic => Ok(ClinvarGermlineAggregateDescription::Pathogenic),
+            pb_query::ClinvarGermlineAggregateDescription::LikelyPathogenic => Ok(ClinvarGermlineAggregateDescription::LikelyPathogenic),
+            pb_query::ClinvarGermlineAggregateDescription::UncertainSignificance => Ok(ClinvarGermlineAggregateDescription::UncertainSignificance),
+            pb_query::ClinvarGermlineAggregateDescription::LikelyBenign => Ok(ClinvarGermlineAggregateDescription::LikelyBenign),
+            pb_query::ClinvarGermlineAggregateDescription::Benign => Ok(ClinvarGermlineAggregateDescription::Benign),
+            _ => Err(clinvar_germline_aggregate_description::Error::UnknownClinvarGermlineAggregateDescriptionValue(value)),
+        }
+    }
+}
+
+/// Query settings for ClinVar.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct QuerySettingsClinVar {
+    /// Whether to require ClinVar membership.
+    pub presence_required: bool,
+    /// The ClinVar germline aggregate description to include.
+    pub germline_descriptions: Vec<ClinvarGermlineAggregateDescription>,
+    /// Whether to include conflicting interpretation ClinVar variants.
+    pub allow_conflicting_interpretations: bool,
+}
+
+/// Supporting code for `QuerySettingsClinVar`.
+pub(crate) mod query_settings_clinvar {
+    /// Error type for `QuerySettingsClinVar::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Cannot convert i32 into protobuf ClinvarGermlineAggregateDescription: {0}")]
+        UnknownClinvarGermlineAggregateDescriptionInt(i32),
+        #[error("Cannot convert protobuf ClinvarGermlineAggregateDescription: {0:?}")]
+        UnknownClinvarGermlineAggregateDescriptionValue(
+            super::pb_query::ClinvarGermlineAggregateDescription,
+        ),
+    }
+}
+
+impl TryFrom<pb_query::QuerySettingsClinVar> for QuerySettingsClinVar {
+    type Error = query_settings_clinvar::Error;
+
+    fn try_from(value: pb_query::QuerySettingsClinVar) -> Result<Self, Self::Error> {
+        let germline_descriptions = value
+            .germline_descriptions
+            .into_iter()
+            .map(|v| {
+                pb_query::ClinvarGermlineAggregateDescription::try_from(v)
+                    .map_err(|_| Self::Error::UnknownClinvarGermlineAggregateDescriptionInt(v))
+            })
+            .collect::<Result<Vec<_>, _>>()?;
+        let germline_descriptions = germline_descriptions
+            .into_iter()
+            .map(|v| {
+                ClinvarGermlineAggregateDescription::try_from(v)
+                    .map_err(|_| Self::Error::UnknownClinvarGermlineAggregateDescriptionValue(v))
+            })
+            .collect::<Result<Vec<_>, _>>()?;
+
+        Ok(Self {
+            presence_required: value.presence_required,
+            germline_descriptions,
+            allow_conflicting_interpretations: value.allow_conflicting_interpretations,
+        })
+    }
+}
+
+/// Query settings for one case.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct CaseQuery {
+    /// Genotype query settings.
+    pub genotype: QuerySettingsGenotype,
+    /// Quality query settings.
+    pub quality: QuerySettingsQuality,
+    /// Frequency query settings.
+    pub frequency: QuerySettingsFrequency,
+    /// Consequence query settings.
+    pub consequence: QuerySettingsConsequence,
+    /// Locus query settings.
+    pub locus: QuerySettingsLocus,
+    /// ClinVar query settings.
+    pub clinvar: QuerySettingsClinVar,
+}
+
+/// Supporting code for `CaseQuery`.
+pub(crate) mod case_query {
+    /// Error type for `CaseQuery::try_from()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum Error {
+        #[error("Missing genotype in protobuf")]
+        GenotypeMissing,
+        #[error("Problem converting protobuf for genotype: {0}")]
+        GenotypeConversion(#[from] super::query_settings_genotype::Error),
+        #[error("Missing quality in protobuf")]
+        QualityMissing,
+        #[error("Problem converting protobuf for quality: {0}")]
+        QualityConversion(#[from] super::query_settings_quality::Error),
+        #[error("Missing frequency in protobuf")]
+        FrequencyMissing,
+        #[error("Problem converting protobuf for frequency: {0}")]
+        FrequencyConversion(#[from] super::query_settings_frequency::Error),
+        #[error("Missing consequence in protobuf")]
+        ConsequenceMissing,
+        #[error("Problem converting protobuf for consequence: {0}")]
+        ConsequenceConversion(#[from] super::query_settings_consequence::Error),
+        #[error("Missing locus in protobuf")]
+        LocusMissing,
+        #[error("Missing clinvar in protobuf")]
+        ClinVarMissing,
+        #[error("Problem converting protobuf for clinvar: {0}")]
+        ClinVarConversion(#[from] super::query_settings_clinvar::Error),
+    }
+}
+
+impl TryFrom<pb_query::CaseQuery> for CaseQuery {
+    type Error = case_query::Error;
+
+    fn try_from(value: pb_query::CaseQuery) -> Result<Self, Self::Error> {
+        let pb_query::CaseQuery {
+            genotype,
+            quality,
+            frequency,
+            consequence,
+            locus,
+            clinvar,
+        } = value;
+
+        let genotype =
+            QuerySettingsGenotype::try_from(genotype.ok_or(Self::Error::GenotypeMissing)?)
+                .map_err(|e| Self::Error::GenotypeConversion(e))?;
+        let quality = QuerySettingsQuality::try_from(quality.ok_or(Self::Error::QualityMissing)?)
+            .map_err(|e| Self::Error::QualityConversion(e))?;
+        let frequency =
+            QuerySettingsFrequency::try_from(frequency.ok_or(Self::Error::FrequencyMissing)?)
+                .map_err(|e| Self::Error::FrequencyConversion(e))?;
+        let consequence =
+            QuerySettingsConsequence::try_from(consequence.ok_or(Self::Error::ConsequenceMissing)?)
+                .map_err(|e| Self::Error::ConsequenceConversion(e))?;
+        let locus = QuerySettingsLocus::from(locus.ok_or(Self::Error::LocusMissing)?);
+        let clinvar = QuerySettingsClinVar::try_from(clinvar.ok_or(Self::Error::ClinVarMissing)?)
+            .map_err(|e| Self::Error::ClinVarConversion(e))?;
+
+        Ok(Self {
+            genotype,
+            quality,
+            frequency,
+            consequence,
+            locus,
+            clinvar,
+        })
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use query_settings_genotype::RecessiveIndexError;
+
+    use super::*;
+
+    #[test]
+    fn test_recessive_mode_try_from() {
+        assert_eq!(
+            RecessiveMode::try_from(pb_query::RecessiveMode::Disabled).unwrap(),
+            RecessiveMode::Disabled
+        );
+        assert_eq!(
+            RecessiveMode::try_from(pb_query::RecessiveMode::CompoundHeterozygous).unwrap(),
+            RecessiveMode::CompoundHeterozygous
+        );
+        assert_eq!(
+            RecessiveMode::try_from(pb_query::RecessiveMode::Homozygous).unwrap(),
+            RecessiveMode::Homozygous
+        );
+        assert_eq!(
+            RecessiveMode::try_from(pb_query::RecessiveMode::Any).unwrap(),
+            RecessiveMode::Any
+        );
+        assert!(RecessiveMode::try_from(pb_query::RecessiveMode::Unspecified).is_err());
+    }
+
+    #[test]
+    fn test_genotype_choice_try_from() {
+        assert_eq!(
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::Any).unwrap(),
+            GenotypeChoice::Any
+        );
+        assert_eq!(
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::Ref).unwrap(),
+            GenotypeChoice::Ref
+        );
+        assert_eq!(
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::Het).unwrap(),
+            GenotypeChoice::Het
+        );
+        assert_eq!(
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::Hom).unwrap(),
+            GenotypeChoice::Hom
+        );
+        assert_eq!(
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::NonHet).unwrap(),
+            GenotypeChoice::NonHet
+        );
+        assert_eq!(
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::NonHom).unwrap(),
+            GenotypeChoice::NonHom
+        );
+        assert_eq!(
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::Variant).unwrap(),
+            GenotypeChoice::Variant
+        );
+        assert_eq!(
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::RecessiveIndex).unwrap(),
+            GenotypeChoice::RecessiveIndex
+        );
+        assert_eq!(
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::RecessiveParent).unwrap(),
+            GenotypeChoice::RecessiveParent
+        );
+        assert!(GenotypeChoice::try_from(pb_query::GenotypeChoice::Unspecified).is_err());
+    }
+
+    #[test]
+    fn test_sample_genotype_choice_try_from() {
+        let pb_sample_genotype_choice = pb_query::SampleGenotypeChoice {
+            sample: "sample".to_string(),
+            genotype: pb_query::GenotypeChoice::Any as i32,
+            include_no_call: true,
+            enabled: true,
+        };
+        let sample_genotype_choice = SampleGenotypeChoice {
+            sample: "sample".to_string(),
+            genotype: GenotypeChoice::Any,
+            include_no_call: true,
+            enabled: true,
+        };
+        assert_eq!(
+            SampleGenotypeChoice::try_from(pb_sample_genotype_choice).unwrap(),
+            sample_genotype_choice
+        );
+    }
+
+    pub mod genotype_choice {
+        use super::GenotypeChoice::{self, *};
+
+        #[rstest::rstest]
+        #[case(Any, &["0", "0/0", "0|0", "1", "1/1", "1|1", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], true)]
+        #[case(Ref, &["0", "0/0", "0|0"], true)]
+        #[case(Ref, &[ "1", "1/1", "1|1", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], false)]
+        #[case(Het, &["0/1", "0|1", "1/0", "1|0"], true)]
+        #[case(Het, &["0", "0/0", "0|0", "1", "1/1", "1|1", ".", "./.", ".|."], false)]
+        #[case(Hom, &["1", "1/1", "1|1"], true)]
+        #[case(Hom, &["0", "0/0", "0|0", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], false)]
+        #[case(NonHom, &["1", "1/1", "1|1"], false)]
+        #[case(NonHom, &["0", "0/0", "0|0", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], true)]
+        #[case(Variant, &["1", "1/1", "1|1", "0/1",  "0|1",  "1/0", "1|0"], true)]
+        #[case(Variant, &["0", "0/0", "0|0", ".", "./.", ".|."], false)]
+        pub fn matches(
+            #[case] genotype_choice: GenotypeChoice,
+            #[case] gt_strs: &[&str],
+            #[case] expected: bool,
+        ) {
+            use crate::seqvars::query::schema::query::MatchesGenotypeStr as _;
+
+            for gt_str in gt_strs {
+                assert_eq!(
+                    genotype_choice.matches(gt_str),
+                    expected,
+                    "{:?} {}",
+                    genotype_choice,
+                    gt_str
+                );
+            }
+        }
+    }
+
+    #[test]
+    fn test_query_settings_genotype_recessive_index_none() {
+        let query_settings_genotype = QuerySettingsGenotype {
+            recessive_mode: RecessiveMode::CompoundHeterozygous,
+            sample_genotypes: Default::default(),
+        };
+
+        assert_eq!(
+            query_settings_genotype.recessive_index(),
+            Err(RecessiveIndexError::NoRecessiveIndexSample)
+        );
+    }
+
+    #[test]
+    fn test_query_settings_genotype_recessive_index_single() {
+        let query_settings_genotype = QuerySettingsGenotype {
+            recessive_mode: RecessiveMode::CompoundHeterozygous,
+            sample_genotypes: indexmap::indexmap! {
+                String::from("sample") => SampleGenotypeChoice {
+                    sample: "sample".to_string(),
+                    genotype: GenotypeChoice::RecessiveIndex,
+                    include_no_call: true,
+                    enabled: true,
+                }
+            },
+        };
+
+        assert_eq!(
+            query_settings_genotype.recessive_index(),
+            Ok(String::from("sample"))
+        );
+    }
+
+    #[test]
+    fn test_query_settings_genotype_recessive_index_two() {
+        let query_settings_genotype = QuerySettingsGenotype {
+            recessive_mode: RecessiveMode::CompoundHeterozygous,
+            sample_genotypes: indexmap::indexmap! {
+                String::from("sample") => SampleGenotypeChoice {
+                    sample: "sample".to_string(),
+                    genotype: GenotypeChoice::RecessiveIndex,
+                    include_no_call: true,
+                    enabled: true,
+                },
+                String::from("sample2") => SampleGenotypeChoice {
+                    sample: "sample2".to_string(),
+                    genotype: GenotypeChoice::RecessiveIndex,
+                    include_no_call: true,
+                    enabled: true,
+                }
+            },
+        };
+
+        assert_eq!(
+            query_settings_genotype.recessive_index(),
+            Err(RecessiveIndexError::MultipleRecessiveIndexSamples(vec![
+                String::from("sample"),
+                String::from("sample2")
+            ]))
+        );
+    }
+
+    #[test]
+    fn test_query_settings_genotype_try_from() {
+        let pb_query_settings_genotype = pb_query::QuerySettingsGenotype {
+            recessive_mode: pb_query::RecessiveMode::Disabled as i32,
+            sample_genotypes: vec![pb_query::SampleGenotypeChoice {
+                sample: "sample".to_string(),
+                genotype: pb_query::GenotypeChoice::Any as i32,
+                include_no_call: true,
+                enabled: true,
+            }],
+        };
+        let query_settings_genotype = QuerySettingsGenotype {
+            recessive_mode: RecessiveMode::Disabled,
+            sample_genotypes: {
+                let mut map = indexmap::IndexMap::new();
+                map.insert(
+                    "sample".to_string(),
+                    SampleGenotypeChoice {
+                        sample: "sample".to_string(),
+                        genotype: GenotypeChoice::Any,
+                        include_no_call: true,
+                        enabled: true,
+                    },
+                );
+                map
+            },
+        };
+        assert_eq!(
+            QuerySettingsGenotype::try_from(pb_query_settings_genotype).unwrap(),
+            query_settings_genotype
+        );
+    }
+
+    #[test]
+    fn test_sample_quality_settings_from() {
+        let pb_sample_quality_settings = pb_query::SampleQualitySettings {
+            sample: "sample".to_string(),
+            filter_active: true,
+            min_dp_het: Some(10),
+            min_dp_hom: Some(20),
+            min_gq: Some(30),
+            min_ab: Some(0.1),
+            min_ad: Some(40),
+            max_ad: Some(50),
+        };
+        let sample_quality_settings = SampleQualitySettings {
+            sample: "sample".to_string(),
+            filter_active: true,
+            min_dp_het: Some(10),
+            min_dp_hom: Some(20),
+            min_gq: Some(30),
+            min_ab: Some(0.1),
+            min_ad: Some(40),
+            max_ad: Some(50),
+        };
+        assert_eq!(
+            SampleQualitySettings::from(pb_sample_quality_settings),
+            sample_quality_settings
+        );
+    }
+
+    #[test]
+    fn test_query_settings_quality_try_from() {
+        let pb_query_settings_quality = pb_query::QuerySettingsQuality {
+            sample_qualities: vec![pb_query::SampleQualitySettings {
+                sample: "sample".to_string(),
+                filter_active: true,
+                min_dp_het: Some(10),
+                min_dp_hom: Some(20),
+                min_gq: Some(30),
+                min_ab: Some(0.1),
+                min_ad: Some(40),
+                max_ad: Some(50),
+            }],
+        };
+        let query_settings_quality = QuerySettingsQuality {
+            sample_qualities: {
+                let mut map = indexmap::IndexMap::new();
+                map.insert(
+                    "sample".to_string(),
+                    SampleQualitySettings {
+                        sample: "sample".to_string(),
+                        filter_active: true,
+                        min_dp_het: Some(10),
+                        min_dp_hom: Some(20),
+                        min_gq: Some(30),
+                        min_ab: Some(0.1),
+                        min_ad: Some(40),
+                        max_ad: Some(50),
+                    },
+                );
+                map
+            },
+        };
+        assert_eq!(
+            QuerySettingsQuality::try_from(pb_query_settings_quality).unwrap(),
+            query_settings_quality
+        );
+    }
+
+    #[test]
+    fn test_gnomad_nuclear_frequency_settings_from() {
+        let pb_gnomad_nuclear_frequency_settings = pb_query::GnomadNuclearFreqyencySettings {
+            enabled: true,
+            heterozygous: Some(10),
+            homozygous: Some(20),
+            hemizygous: Some(30),
+            frequency: Some(0.1),
+        };
+        let gnomad_nuclear_frequency_settings = GnomadNuclearFrequencySettings {
+            enabled: true,
+            heterozygous: Some(10),
+            homozygous: Some(20),
+            hemizygous: Some(30),
+            frequency: Some(0.1),
+        };
+        assert_eq!(
+            GnomadNuclearFrequencySettings::from(pb_gnomad_nuclear_frequency_settings),
+            gnomad_nuclear_frequency_settings
+        );
+    }
+
+    #[test]
+    fn test_gnomad_mitochondrial_frequency_settings_from() {
+        let pb_gnomad_mitochondrial_frequency_settings =
+            pb_query::GnomadMitochondrialFrequencySettings {
+                enabled: true,
+                heteroplasmic: Some(10),
+                homoplasmic: Some(20),
+                frequency: Some(0.1),
+            };
+        let gnomad_mitochondrial_frequency_settings = GnomadMitochondrialFrequencySettings {
+            enabled: true,
+            heteroplasmic: Some(10),
+            homoplasmic: Some(20),
+            frequency: Some(0.1),
+        };
+        assert_eq!(
+            GnomadMitochondrialFrequencySettings::from(pb_gnomad_mitochondrial_frequency_settings),
+            gnomad_mitochondrial_frequency_settings
+        );
+    }
+
+    #[test]
+    fn test_helix_mtdb_frequency_settings_from() {
+        let pb_helix_mtdb_frequency_settings = pb_query::HelixMtDbFrequencySettings {
+            enabled: true,
+            heteroplasmic: Some(10),
+            homoplasmic: Some(20),
+            frequency: Some(0.1),
+        };
+        let helix_mtdb_frequency_settings = HelixMtDbFrequencySettings {
+            enabled: true,
+            heteroplasmic: Some(10),
+            homoplasmic: Some(20),
+            frequency: Some(0.1),
+        };
+        assert_eq!(
+            HelixMtDbFrequencySettings::from(pb_helix_mtdb_frequency_settings),
+            helix_mtdb_frequency_settings
+        );
+    }
+
+    #[test]
+    fn test_inhouse_frequency_settings_from() {
+        let pb_inhouse_frequency_settings = pb_query::InhouseFrequencySettings {
+            enabled: true,
+            heterozygous: Some(10),
+            homozygous: Some(20),
+            hemizygous: Some(30),
+            carriers: Some(40),
+        };
+        let inhouse_frequency_settings = InhouseFrequencySettings {
+            enabled: true,
+            heterozygous: Some(10),
+            homozygous: Some(20),
+            hemizygous: Some(30),
+            carriers: Some(40),
+        };
+        assert_eq!(
+            InhouseFrequencySettings::from(pb_inhouse_frequency_settings),
+            inhouse_frequency_settings
+        );
+    }
+
+    #[test]
+    fn test_query_settings_frequency_try_from() {
+        let pb_query_settings_frequency = pb_query::QuerySettingsFrequency {
+            gnomad_exomes: Some(pb_query::GnomadNuclearFreqyencySettings {
+                enabled: true,
+                heterozygous: Some(10),
+                homozygous: Some(20),
+                hemizygous: Some(30),
+                frequency: Some(0.1),
+            }),
+            gnomad_genomes: Some(pb_query::GnomadNuclearFreqyencySettings {
+                enabled: true,
+                heterozygous: Some(10),
+                homozygous: Some(20),
+                hemizygous: Some(30),
+                frequency: Some(0.1),
+            }),
+            gnomad_mt: Some(pb_query::GnomadMitochondrialFrequencySettings {
+                enabled: true,
+                heteroplasmic: Some(10),
+                homoplasmic: Some(20),
+                frequency: Some(0.1),
+            }),
+            helixmtdb: Some(pb_query::HelixMtDbFrequencySettings {
+                enabled: true,
+                heteroplasmic: Some(10),
+                homoplasmic: Some(20),
+                frequency: Some(0.1),
+            }),
+            inhouse: Some(pb_query::InhouseFrequencySettings {
+                enabled: true,
+                heterozygous: Some(10),
+                homozygous: Some(20),
+                hemizygous: Some(30),
+                carriers: Some(40),
+            }),
+        };
+        let query_settings_frequency = QuerySettingsFrequency {
+            gnomad_exomes: GnomadNuclearFrequencySettings {
+                enabled: true,
+                heterozygous: Some(10),
+                homozygous: Some(20),
+                hemizygous: Some(30),
+                frequency: Some(0.1),
+            },
+            gnomad_genomes: GnomadNuclearFrequencySettings {
+                enabled: true,
+                heterozygous: Some(10),
+                homozygous: Some(20),
+                hemizygous: Some(30),
+                frequency: Some(0.1),
+            },
+            gnomad_mt: GnomadMitochondrialFrequencySettings {
+                enabled: true,
+                heteroplasmic: Some(10),
+                homoplasmic: Some(20),
+                frequency: Some(0.1),
+            },
+            helixmtdb: HelixMtDbFrequencySettings {
+                enabled: true,
+                heteroplasmic: Some(10),
+                homoplasmic: Some(20),
+                frequency: Some(0.1),
+            },
+            inhouse: InhouseFrequencySettings {
+                enabled: true,
+                heterozygous: Some(10),
+                homozygous: Some(20),
+                hemizygous: Some(30),
+                carriers: Some(40),
+            },
+        };
+        assert_eq!(
+            QuerySettingsFrequency::try_from(pb_query_settings_frequency).unwrap(),
+            query_settings_frequency
+        );
+    }
+
+    #[test]
+    fn test_variant_type_try_from() {
+        assert_eq!(
+            VariantType::try_from(pb_query::VariantType::Snv).unwrap(),
+            VariantType::Snv
+        );
+        assert_eq!(
+            VariantType::try_from(pb_query::VariantType::Indel).unwrap(),
+            VariantType::Indel
+        );
+        assert_eq!(
+            VariantType::try_from(pb_query::VariantType::Mnv).unwrap(),
+            VariantType::Mnv
+        );
+        assert_eq!(
+            VariantType::try_from(pb_query::VariantType::ComplexSubstitution).unwrap(),
+            VariantType::ComplexSubstitution
+        );
+        assert!(VariantType::try_from(pb_query::VariantType::Unspecified).is_err());
+    }
+
+    #[test]
+    fn test_transcript_type_try_from() {
+        assert_eq!(
+            TranscriptType::try_from(pb_query::TranscriptType::Coding).unwrap(),
+            TranscriptType::Coding
+        );
+        assert_eq!(
+            TranscriptType::try_from(pb_query::TranscriptType::NonCoding).unwrap(),
+            TranscriptType::NonCoding
+        );
+        assert!(TranscriptType::try_from(pb_query::TranscriptType::Unspecified).is_err());
+    }
+
+    #[test]
+    fn test_consequence_try_from() {
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::TranscriptAblation).unwrap(),
+            Consequence::TranscriptAblation
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::ExonLossVariant).unwrap(),
+            Consequence::ExonLossVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::SpliceAcceptorVariant).unwrap(),
+            Consequence::SpliceAcceptorVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::SpliceDonorVariant).unwrap(),
+            Consequence::SpliceDonorVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::StopGained).unwrap(),
+            Consequence::StopGained
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::FrameshiftVariant).unwrap(),
+            Consequence::FrameshiftVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::StopLost).unwrap(),
+            Consequence::StopLost
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::StartLost).unwrap(),
+            Consequence::StartLost
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::TranscriptAmplification).unwrap(),
+            Consequence::TranscriptAmplification
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::DisruptiveInframeInsertion).unwrap(),
+            Consequence::DisruptiveInframeInsertion
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::DisruptiveInframeDeletion).unwrap(),
+            Consequence::DisruptiveInframeDeletion
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::ConservativeInframeInsertion).unwrap(),
+            Consequence::ConservativeInframeInsertion
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::ConservativeInframeDeletion).unwrap(),
+            Consequence::ConservativeInframeDeletion
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::MissenseVariant).unwrap(),
+            Consequence::MissenseVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::SpliceDonorFifthBaseVariant).unwrap(),
+            Consequence::SpliceDonorFifthBaseVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::SpliceRegionVariant).unwrap(),
+            Consequence::SpliceRegionVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::SpliceDonorRegionVariant).unwrap(),
+            Consequence::SpliceDonorRegionVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::SplicePolypyrimidineTractVariant).unwrap(),
+            Consequence::SplicePolypyrimidineTractVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::StartRetainedVariant).unwrap(),
+            Consequence::StartRetainedVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::StopRetainedVariant).unwrap(),
+            Consequence::StopRetainedVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::SynonymousVariant).unwrap(),
+            Consequence::SynonymousVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::CodingSequenceVariant).unwrap(),
+            Consequence::CodingSequenceVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::FivePrimeUtrExonVariant).unwrap(),
+            Consequence::FivePrimeUtrExonVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::FivePrimeUtrIntronVariant).unwrap(),
+            Consequence::FivePrimeUtrIntronVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::ThreePrimeUtrExonVariant).unwrap(),
+            Consequence::ThreePrimeUtrExonVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::ThreePrimeUtrIntronVariant).unwrap(),
+            Consequence::ThreePrimeUtrIntronVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::NonCodingTranscriptExonVariant).unwrap(),
+            Consequence::NonCodingTranscriptExonVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::NonCodingTranscriptIntronVariant).unwrap(),
+            Consequence::NonCodingTranscriptIntronVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::UpstreamGeneVariant).unwrap(),
+            Consequence::UpstreamGeneVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::DownstreamGeneVariant).unwrap(),
+            Consequence::DownstreamGeneVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::IntergenicVariant).unwrap(),
+            Consequence::IntergenicVariant
+        );
+        assert_eq!(
+            Consequence::try_from(pb_query::Consequence::IntronVariant).unwrap(),
+            Consequence::IntronVariant
+        );
+        assert!(Consequence::try_from(pb_query::Consequence::Unspecified).is_err());
+    }
+
+    #[test]
+    fn test_query_settings_consequence_try_from() {
+        let pb_query_settings_consequence = pb_query::QuerySettingsConsequence {
+            variant_types: vec![
+                pb_query::VariantType::Unspecified as i32,
+                pb_query::VariantType::Snv as i32,
+                pb_query::VariantType::Indel as i32,
+                pb_query::VariantType::Mnv as i32,
+                pb_query::VariantType::ComplexSubstitution as i32,
+            ],
+            transcript_types: vec![
+                pb_query::TranscriptType::Coding as i32,
+                pb_query::TranscriptType::NonCoding as i32,
+            ],
+            consequences: vec![
+                pb_query::Consequence::TranscriptAblation as i32,
+                pb_query::Consequence::ExonLossVariant as i32,
+                pb_query::Consequence::SpliceAcceptorVariant as i32,
+                pb_query::Consequence::SpliceDonorVariant as i32,
+                pb_query::Consequence::StopGained as i32,
+                pb_query::Consequence::FrameshiftVariant as i32,
+                pb_query::Consequence::StopLost as i32,
+                pb_query::Consequence::StartLost as i32,
+            ],
+            max_dist_to_exon: Some(10),
+        };
+        let query_settings_consequence = QuerySettingsConsequence {
+            variant_types: vec![
+                VariantType::Snv,
+                VariantType::Indel,
+                VariantType::Mnv,
+                VariantType::ComplexSubstitution,
+            ],
+            transcript_types: vec![TranscriptType::Coding, TranscriptType::NonCoding],
+            consequences: vec![
+                Consequence::TranscriptAblation,
+                Consequence::ExonLossVariant,
+                Consequence::SpliceAcceptorVariant,
+                Consequence::SpliceDonorVariant,
+                Consequence::StopGained,
+                Consequence::FrameshiftVariant,
+                Consequence::StopLost,
+                Consequence::StartLost,
+            ],
+            max_dist_to_exon: Some(10),
+        };
+        assert_eq!(
+            QuerySettingsConsequence::try_from(pb_query_settings_consequence).unwrap(),
+            query_settings_consequence
+        );
+    }
+
+    #[test]
+    fn test_range_from() {
+        let pb_range = pb_query::Range { start: 1, end: 2 };
+        let range = Range { start: 1, end: 2 };
+        assert_eq!(Range::from(pb_range), range);
+    }
+
+    #[test]
+    fn test_genomic_region_from() {
+        let pb_genomic_region = pb_query::GenomicRegion {
+            chrom: "chrom".to_string(),
+            range: Some(pb_query::Range { start: 1, end: 2 }),
+        };
+        let genomic_region = GenomicRegion {
+            chrom: "chrom".to_string(),
+            range: Some(Range { start: 1, end: 2 }),
+        };
+        assert_eq!(GenomicRegion::from(pb_genomic_region), genomic_region);
+    }
+
+    #[test]
+    fn test_query_settings_locus_from() {
+        let pb_query_settings_locus = pb_query::QuerySettingsLocus {
+            genes: vec!["gene".to_string()],
+            genome_regions: vec![pb_query::GenomicRegion {
+                chrom: "chrom".to_string(),
+                range: Some(pb_query::Range { start: 1, end: 2 }),
+            }],
+        };
+        let query_settings_locus = QuerySettingsLocus {
+            genes: vec!["gene".to_string()],
+            genome_regions: vec![GenomicRegion {
+                chrom: "chrom".to_string(),
+                range: Some(Range { start: 1, end: 2 }),
+            }],
+        };
+        assert_eq!(
+            QuerySettingsLocus::from(pb_query_settings_locus),
+            query_settings_locus
+        );
+    }
+
+    #[test]
+    fn test_clinvar_germline_aggregate_description_try_from() {
+        assert_eq!(
+            ClinvarGermlineAggregateDescription::try_from(
+                pb_query::ClinvarGermlineAggregateDescription::Pathogenic
+            )
+            .unwrap(),
+            ClinvarGermlineAggregateDescription::Pathogenic
+        );
+        assert_eq!(
+            ClinvarGermlineAggregateDescription::try_from(
+                pb_query::ClinvarGermlineAggregateDescription::LikelyPathogenic
+            )
+            .unwrap(),
+            ClinvarGermlineAggregateDescription::LikelyPathogenic
+        );
+        assert_eq!(
+            ClinvarGermlineAggregateDescription::try_from(
+                pb_query::ClinvarGermlineAggregateDescription::UncertainSignificance
+            )
+            .unwrap(),
+            ClinvarGermlineAggregateDescription::UncertainSignificance
+        );
+        assert_eq!(
+            ClinvarGermlineAggregateDescription::try_from(
+                pb_query::ClinvarGermlineAggregateDescription::LikelyBenign
+            )
+            .unwrap(),
+            ClinvarGermlineAggregateDescription::LikelyBenign
+        );
+        assert_eq!(
+            ClinvarGermlineAggregateDescription::try_from(
+                pb_query::ClinvarGermlineAggregateDescription::Benign
+            )
+            .unwrap(),
+            ClinvarGermlineAggregateDescription::Benign
+        );
+        assert!(ClinvarGermlineAggregateDescription::try_from(
+            pb_query::ClinvarGermlineAggregateDescription::Unspecified
+        )
+        .is_err());
+    }
+
+    #[test]
+    fn test_query_settings_clinvar_try_from() {
+        let pb_query_settings_clinvar = pb_query::QuerySettingsClinVar {
+            presence_required: true,
+            germline_descriptions: vec![
+                pb_query::ClinvarGermlineAggregateDescription::Pathogenic as i32,
+                pb_query::ClinvarGermlineAggregateDescription::LikelyPathogenic as i32,
+            ],
+            allow_conflicting_interpretations: true,
+        };
+        let query_settings_clinvar = QuerySettingsClinVar {
+            presence_required: true,
+            germline_descriptions: vec![
+                ClinvarGermlineAggregateDescription::Pathogenic,
+                ClinvarGermlineAggregateDescription::LikelyPathogenic,
+            ],
+            allow_conflicting_interpretations: true,
+        };
+        assert_eq!(
+            QuerySettingsClinVar::try_from(pb_query_settings_clinvar).unwrap(),
+            query_settings_clinvar
+        );
+    }
+
+    #[test]
+    fn test_case_query_try_from() {
+        let pb_case_query = pb_query::CaseQuery {
+            genotype: Some(pb_query::QuerySettingsGenotype {
+                recessive_mode: pb_query::RecessiveMode::Disabled as i32,
+                sample_genotypes: vec![pb_query::SampleGenotypeChoice {
+                    sample: "sample".to_string(),
+                    genotype: pb_query::GenotypeChoice::Any as i32,
+                    include_no_call: true,
+                    enabled: true,
+                }],
+            }),
+            quality: Some(pb_query::QuerySettingsQuality {
+                sample_qualities: vec![pb_query::SampleQualitySettings {
+                    sample: "sample".to_string(),
+                    filter_active: true,
+                    min_dp_het: Some(10),
+                    min_dp_hom: Some(20),
+                    min_gq: Some(30),
+                    min_ab: Some(0.1),
+                    min_ad: Some(40),
+                    max_ad: Some(50),
+                }],
+            }),
+            frequency: Some(pb_query::QuerySettingsFrequency {
+                gnomad_exomes: Some(pb_query::GnomadNuclearFreqyencySettings {
+                    enabled: true,
+                    heterozygous: Some(10),
+                    homozygous: Some(20),
+                    hemizygous: Some(30),
+                    frequency: Some(0.1),
+                }),
+                gnomad_genomes: Some(pb_query::GnomadNuclearFreqyencySettings {
+                    enabled: true,
+                    heterozygous: Some(10),
+                    homozygous: Some(20),
+                    hemizygous: Some(30),
+                    frequency: Some(0.1),
+                }),
+                gnomad_mt: Some(pb_query::GnomadMitochondrialFrequencySettings {
+                    enabled: true,
+                    heteroplasmic: Some(10),
+                    homoplasmic: Some(20),
+                    frequency: Some(0.1),
+                }),
+                helixmtdb: Some(pb_query::HelixMtDbFrequencySettings {
+                    enabled: true,
+                    heteroplasmic: Some(10),
+                    homoplasmic: Some(20),
+                    frequency: Some(0.1),
+                }),
+                inhouse: Some(pb_query::InhouseFrequencySettings {
+                    enabled: true,
+                    heterozygous: Some(10),
+                    homozygous: Some(20),
+                    hemizygous: Some(30),
+                    carriers: Some(40),
+                }),
+            }),
+            consequence: Some(pb_query::QuerySettingsConsequence {
+                variant_types: vec![
+                    pb_query::VariantType::Unspecified as i32,
+                    pb_query::VariantType::Snv as i32,
+                    pb_query::VariantType::Indel as i32,
+                    pb_query::VariantType::Mnv as i32,
+                    pb_query::VariantType::ComplexSubstitution as i32,
+                ],
+                transcript_types: vec![
+                    pb_query::TranscriptType::Coding as i32,
+                    pb_query::TranscriptType::NonCoding as i32,
+                ],
+                consequences: vec![
+                    pb_query::Consequence::TranscriptAblation as i32,
+                    pb_query::Consequence::ExonLossVariant as i32,
+                    pb_query::Consequence::SpliceAcceptorVariant as i32,
+                    pb_query::Consequence::SpliceDonorVariant as i32,
+                    pb_query::Consequence::StopGained as i32,
+                    pb_query::Consequence::FrameshiftVariant as i32,
+                    pb_query::Consequence::StopLost as i32,
+                    pb_query::Consequence::StartLost as i32,
+                ],
+                max_dist_to_exon: Some(10),
+            }),
+            locus: Some(pb_query::QuerySettingsLocus {
+                genes: vec!["gene".to_string()],
+                genome_regions: vec![pb_query::GenomicRegion {
+                    chrom: "chrom".to_string(),
+                    range: Some(pb_query::Range { start: 1, end: 2 }),
+                }],
+            }),
+            clinvar: Some(pb_query::QuerySettingsClinVar {
+                presence_required: true,
+                germline_descriptions: vec![
+                    pb_query::ClinvarGermlineAggregateDescription::Pathogenic as i32,
+                    pb_query::ClinvarGermlineAggregateDescription::LikelyPathogenic as i32,
+                ],
+                allow_conflicting_interpretations: true,
+            }),
+        };
+        let case_query = CaseQuery {
+            genotype: QuerySettingsGenotype {
+                recessive_mode: RecessiveMode::Disabled,
+                sample_genotypes: {
+                    let mut map = indexmap::IndexMap::new();
+                    map.insert(
+                        "sample".to_string(),
+                        SampleGenotypeChoice {
+                            sample: "sample".to_string(),
+                            genotype: GenotypeChoice::Any,
+                            include_no_call: true,
+                            enabled: true,
+                        },
+                    );
+                    map
+                },
+            },
+            quality: QuerySettingsQuality {
+                sample_qualities: {
+                    let mut map = indexmap::IndexMap::new();
+                    map.insert(
+                        "sample".to_string(),
+                        SampleQualitySettings {
+                            sample: "sample".to_string(),
+                            filter_active: true,
+                            min_dp_het: Some(10),
+                            min_dp_hom: Some(20),
+                            min_gq: Some(30),
+                            min_ab: Some(0.1),
+                            min_ad: Some(40),
+                            max_ad: Some(50),
+                        },
+                    );
+                    map
+                },
+            },
+            frequency: QuerySettingsFrequency {
+                gnomad_exomes: GnomadNuclearFrequencySettings {
+                    enabled: true,
+                    heterozygous: Some(10),
+                    homozygous: Some(20),
+                    hemizygous: Some(30),
+                    frequency: Some(0.1),
+                },
+                gnomad_genomes: GnomadNuclearFrequencySettings {
+                    enabled: true,
+                    heterozygous: Some(10),
+                    homozygous: Some(20),
+                    hemizygous: Some(30),
+                    frequency: Some(0.1),
+                },
+                gnomad_mt: GnomadMitochondrialFrequencySettings {
+                    enabled: true,
+                    heteroplasmic: Some(10),
+                    homoplasmic: Some(20),
+                    frequency: Some(0.1),
+                },
+                helixmtdb: HelixMtDbFrequencySettings {
+                    enabled: true,
+                    heteroplasmic: Some(10),
+                    homoplasmic: Some(20),
+                    frequency: Some(0.1),
+                },
+                inhouse: InhouseFrequencySettings {
+                    enabled: true,
+                    heterozygous: Some(10),
+                    homozygous: Some(20),
+                    hemizygous: Some(30),
+                    carriers: Some(40),
+                },
+            },
+            consequence: QuerySettingsConsequence {
+                variant_types: vec![
+                    VariantType::Snv,
+                    VariantType::Indel,
+                    VariantType::Mnv,
+                    VariantType::ComplexSubstitution,
+                ],
+                transcript_types: vec![TranscriptType::Coding, TranscriptType::NonCoding],
+                consequences: vec![
+                    Consequence::TranscriptAblation,
+                    Consequence::ExonLossVariant,
+                    Consequence::SpliceAcceptorVariant,
+                    Consequence::SpliceDonorVariant,
+                    Consequence::StopGained,
+                    Consequence::FrameshiftVariant,
+                    Consequence::StopLost,
+                    Consequence::StartLost,
+                ],
+                max_dist_to_exon: Some(10),
+            },
+            locus: QuerySettingsLocus {
+                genes: vec!["gene".to_string()],
+                genome_regions: vec![GenomicRegion {
+                    chrom: "chrom".to_string(),
+                    range: Some(Range { start: 1, end: 2 }),
+                }],
+            },
+            clinvar: QuerySettingsClinVar {
+                presence_required: true,
+                germline_descriptions: vec![
+                    ClinvarGermlineAggregateDescription::Pathogenic,
+                    ClinvarGermlineAggregateDescription::LikelyPathogenic,
+                ],
+                allow_conflicting_interpretations: true,
+            },
+        };
+        assert_eq!(CaseQuery::try_from(pb_case_query).unwrap(), case_query);
+    }
+
+    #[rstest::rstest]
+    #[case("tests/seqvars/query/empty")]
+    #[case("tests/seqvars/query/full")]
+    #[case("tests/seqvars/query/with_extra")]
+    pub fn smoke_test_load(#[case] path_input: &str) -> Result<(), anyhow::Error> {
+        mehari::common::set_snapshot_suffix!("{}.json", path_input.split('/').last().unwrap());
+
+        let query: super::CaseQuery =
+            serde_json::from_reader(std::fs::File::open(format!("{}.json", path_input))?)?;
+
+        if !path_input.contains("with_extra") {
+            // Check if pbjson loading yields same result
+            let query_pb: crate::pbs::varfish::v1::seqvars::query::CaseQuery =
+                serde_json::from_reader(std::fs::File::open(format!("{}-pb.json", path_input))?)?;
+            let query_pb_conv = super::CaseQuery::try_from(query_pb)?;
+            assert_eq!(query, query_pb_conv);
+        }
+        insta::assert_yaml_snapshot!(&query);
+
+        Ok(())
+    }
+}
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap
deleted file mode 100644
index ead427e8..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap
+++ /dev/null
@@ -1,156 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41273700
-reference: C
-alternative: CA
-ann_fields:
-  - allele:
-      Alt:
-        alternative: CA
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007294.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 2
-      total: 22
-    hgvs_t: c.80+2333_80+2334insT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 193
-      total: 7088
-    cds_pos:
-      ord: 80
-      total: 5592
-    protein_pos: ~
-    distance: 2333
-    messages: ~
-  - allele:
-      Alt:
-        alternative: CA
-    consequences:
-      - 5_prime_UTR_variant
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007297.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 2
-      total: 21
-    hgvs_t: c.-8+2333_-8+2334insT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 187
-      total: 7028
-    cds_pos:
-      ord: -8
-      total: 5451
-    protein_pos: ~
-    distance: 2333
-    messages: ~
-  - allele:
-      Alt:
-        alternative: CA
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007299.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 2
-      total: 21
-    hgvs_t: c.80+2333_80+2334insT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 187
-      total: 3696
-    cds_pos:
-      ord: 80
-      total: 2100
-    protein_pos: ~
-    distance: 2333
-    messages: ~
-  - allele:
-      Alt:
-        alternative: CA
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007300.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 2
-      total: 23
-    hgvs_t: c.80+2333_80+2334insT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 193
-      total: 7151
-    cds_pos:
-      ord: 80
-      total: 5655
-    protein_pos: ~
-    distance: 2333
-    messages: ~
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 42
-    dp: 14
-    ad: 0
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 10
-    dp: 7
-    ad: 1
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /0/1
-    quality: 65
-    dp: 10
-    ad: 5
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap
deleted file mode 100644
index 915b4386..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 73
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 3975
-    ad: 0
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 2871
-    ad: 2871
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 3320
-    ad: 3320
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap
deleted file mode 100644
index 781b0139..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 119
-reference: T
-alternative: C
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 5418
-    ad: 1
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 4039
-    ad: 4039
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 4113
-    ad: 4112
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap
deleted file mode 100644
index ab498001..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 189
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 3069
-    ad: 0
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 1721
-    ad: 1721
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 2204
-    ad: 2204
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap
deleted file mode 100644
index 2d5a3119..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
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----
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap
deleted file mode 100644
index 600682cb..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap
deleted file mode 100644
index ff9c3f92..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap
deleted file mode 100644
index 4696d17d..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 263
-reference: A
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap
deleted file mode 100644
index 3d05e063..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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-reference: A
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-inhouse_het: 0
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap
deleted file mode 100644
index 990786b9..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 310
-reference: T
-alternative: TC
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap
deleted file mode 100644
index 9a87b987..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap
+++ /dev/null
@@ -1,155 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41252332
-reference: T
-alternative: C
-ann_fields:
-  - allele:
-      Alt:
-        alternative: C
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
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-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 22
-    hgvs_t: c.442-435A>G
-    hgvs_p: p.?
-    tx_pos:
-      ord: 555
-      total: 7088
-    cds_pos:
-      ord: 442
-      total: 5592
-    protein_pos: ~
-    distance: -434
-    messages: ~
-  - allele:
-      Alt:
-        alternative: C
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007297.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 5
-      total: 21
-    hgvs_t: c.301-435A>G
-    hgvs_p: p.?
-    tx_pos:
-      ord: 495
-      total: 7028
-    cds_pos:
-      ord: 301
-      total: 5451
-    protein_pos: ~
-    distance: -434
-    messages: ~
-  - allele:
-      Alt:
-        alternative: C
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007299.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 21
-    hgvs_t: c.442-435A>G
-    hgvs_p: p.?
-    tx_pos:
-      ord: 549
-      total: 3696
-    cds_pos:
-      ord: 442
-      total: 2100
-    protein_pos: ~
-    distance: -434
-    messages: ~
-  - allele:
-      Alt:
-        alternative: C
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
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-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007300.4
-    feature_biotype:
-      - Coding
-    rank:
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-      total: 23
-    hgvs_t: c.442-435A>G
-    hgvs_p: p.?
-    tx_pos:
-      ord: 555
-      total: 7151
-    cds_pos:
-      ord: 442
-      total: 5655
-    protein_pos: ~
-    distance: -434
-    messages: ~
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap
deleted file mode 100644
index 6a7e3b22..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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-reference: T
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-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap
deleted file mode 100644
index dca82aa0..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 709
-reference: G
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-  Case_1_father-N1-DNA1-WGS1:
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap
deleted file mode 100644
index 5aa61fec..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 750
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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-    genotype: /1/1
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap
deleted file mode 100644
index 17d1f425..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 879
-reference: T
-alternative: C
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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-inhouse_het: 0
-inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap
deleted file mode 100644
index 81c3c6e4..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap
deleted file mode 100644
index af3a87fd..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap
deleted file mode 100644
index 904e7ea2..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 1824
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap
deleted file mode 100644
index bfa7b0ca..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 2633
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap
deleted file mode 100644
index 1568e48f..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 2706
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-  Case_1_father-N1-DNA1-WGS1:
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap
deleted file mode 100644
index e0dca656..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 3010
-reference: G
-alternative: A
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap
deleted file mode 100644
index e99e8bc6..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap
+++ /dev/null
@@ -1,155 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41252691
-reference: ATATAAT
-alternative: A
-ann_fields:
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007294.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
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-    hgvs_t: c.442-800_442-795delATTATA
-    hgvs_p: p.?
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-      ord: 555
-      total: 7088
-    cds_pos:
-      ord: 442
-      total: 5592
-    protein_pos: ~
-    distance: -794
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007297.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 5
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-    hgvs_t: c.301-800_301-795delATTATA
-    hgvs_p: p.?
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-      total: 7028
-    cds_pos:
-      ord: 301
-      total: 5451
-    protein_pos: ~
-    distance: -794
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007299.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 21
-    hgvs_t: c.442-800_442-795delATTATA
-    hgvs_p: p.?
-    tx_pos:
-      ord: 549
-      total: 3696
-    cds_pos:
-      ord: 442
-      total: 2100
-    protein_pos: ~
-    distance: -794
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007300.4
-    feature_biotype:
-      - Coding
-    rank:
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-    hgvs_t: c.442-800_442-795delATTATA
-    hgvs_p: p.?
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-      total: 7151
-    cds_pos:
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-      total: 5655
-    protein_pos: ~
-    distance: -794
-    messages: ~
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-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap
deleted file mode 100644
index c3f7b67e..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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-inhouse_hom: 0
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap
deleted file mode 100644
index 6566cd19..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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-inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap
deleted file mode 100644
index 8574d6c9..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 4769
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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-  Case_1_mother-N1-DNA1-WGS1:
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap
deleted file mode 100644
index 5959b3be..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 5046
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-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap
deleted file mode 100644
index 7d472bfb..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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-reference: G
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-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 1970
-    ad: 1968
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap
deleted file mode 100644
index d4d9dd52..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 7028
-reference: C
-alternative: T
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 2580
-    ad: 3
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 2203
-    ad: 2201
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 1946
-    ad: 1945
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap
deleted file mode 100644
index 79819260..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 7864
-reference: C
-alternative: T
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 3589
-    ad: 1
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 3465
-    ad: 3465
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 2746
-    ad: 2746
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap
deleted file mode 100644
index c64b674a..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 8170
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 2052
-    ad: 1
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 2257
-    ad: 2257
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 1774
-    ad: 1774
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap
deleted file mode 100644
index 1e787feb..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 8251
-reference: G
-alternative: A
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 2360
-    ad: 0
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 2317
-    ad: 2317
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 1625
-    ad: 1624
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap
deleted file mode 100644
index 334983e8..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 8860
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 3278
-    ad: 3278
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 3088
-    ad: 3088
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 2241
-    ad: 2241
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap
deleted file mode 100644
index 43a5f962..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap
+++ /dev/null
@@ -1,155 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41252693
-reference: ATAAT
-alternative: A
-ann_fields:
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007294.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 22
-    hgvs_t: c.442-800_442-797delATTA
-    hgvs_p: p.?
-    tx_pos:
-      ord: 555
-      total: 7088
-    cds_pos:
-      ord: 442
-      total: 5592
-    protein_pos: ~
-    distance: -796
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007297.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 5
-      total: 21
-    hgvs_t: c.301-800_301-797delATTA
-    hgvs_p: p.?
-    tx_pos:
-      ord: 495
-      total: 7028
-    cds_pos:
-      ord: 301
-      total: 5451
-    protein_pos: ~
-    distance: -796
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007299.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 21
-    hgvs_t: c.442-800_442-797delATTA
-    hgvs_p: p.?
-    tx_pos:
-      ord: 549
-      total: 3696
-    cds_pos:
-      ord: 442
-      total: 2100
-    protein_pos: ~
-    distance: -796
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007300.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 23
-    hgvs_t: c.442-800_442-797delATTA
-    hgvs_p: p.?
-    tx_pos:
-      ord: 555
-      total: 7151
-    cds_pos:
-      ord: 442
-      total: 5655
-    protein_pos: ~
-    distance: -796
-    messages: ~
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 27
-    dp: 9
-    ad: 0
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 42
-    dp: 14
-    ad: 0
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /0/1
-    quality: 99
-    dp: 22
-    ad: 11
-    phasing_id: ~
-gnomad_exomes_an: 3866
-gnomad_exomes_hom: 244
-gnomad_exomes_het: 618
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap
deleted file mode 100644
index 9203ccc6..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 8994
-reference: G
-alternative: A
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 2793
-    ad: 0
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 2368
-    ad: 2368
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 1918
-    ad: 1917
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap
deleted file mode 100644
index f3d3be09..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 9007
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 2959
-    ad: 2959
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 2442
-    ad: 0
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 1735
-    ad: 0
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap
deleted file mode 100644
index 15091766..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 9150
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 3163
-    ad: 3163
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 3538
-    ad: 0
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 2767
-    ad: 0
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap
deleted file mode 100644
index 1a9bf9a1..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 9380
-reference: G
-alternative: A
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 3321
-    ad: 3320
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 3222
-    ad: 0
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 2547
-    ad: 0
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap
deleted file mode 100644
index 4522b5a2..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 10097
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 2660
-    ad: 0
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /0/1
-    quality: 99
-    dp: 2188
-    ad: 508
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 1851
-    ad: 0
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
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-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap
deleted file mode 100644
index f20b6f09..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
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----
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-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap
deleted file mode 100644
index e60b17f1..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 11674
-reference: C
-alternative: T
-ann_fields: []
-call_info:
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-gnomad_exomes_hom: 0
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-inhouse_an: 0
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap
deleted file mode 100644
index 26e1826a..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 11719
-reference: G
-alternative: A
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap
deleted file mode 100644
index 112aaa62..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 11947
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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-    ad: 1804
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-gnomad_exomes_hom: 0
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap
deleted file mode 100644
index e8a8c2dc..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 12414
-reference: T
-alternative: C
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
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-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/1
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-gnomad_exomes_hom: 0
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-inhouse_an: 0
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-inhouse_het: 0
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap
deleted file mode 100644
index 24837d66..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap
+++ /dev/null
@@ -1,156 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41252695
-reference: AAT
-alternative: A
-ann_fields:
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007294.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 22
-    hgvs_t: c.442-800_442-799delAT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 555
-      total: 7088
-    cds_pos:
-      ord: 442
-      total: 5592
-    protein_pos: ~
-    distance: -798
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007297.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 5
-      total: 21
-    hgvs_t: c.301-800_301-799delAT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 495
-      total: 7028
-    cds_pos:
-      ord: 301
-      total: 5451
-    protein_pos: ~
-    distance: -798
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007299.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 21
-    hgvs_t: c.442-800_442-799delAT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 549
-      total: 3696
-    cds_pos:
-      ord: 442
-      total: 2100
-    protein_pos: ~
-    distance: -798
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007300.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 23
-    hgvs_t: c.442-800_442-799delAT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 555
-      total: 7151
-    cds_pos:
-      ord: 442
-      total: 5655
-    protein_pos: ~
-    distance: -798
-    messages: ~
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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-  Case_1_mother-N1-DNA1-WGS1:
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-
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap
deleted file mode 100644
index 05d718ce..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 12648
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap
deleted file mode 100644
index e1928baa..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 12705
-reference: C
-alternative: T
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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-  Case_1_mother-N1-DNA1-WGS1:
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap
deleted file mode 100644
index c2fc5416..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 13406
-reference: G
-alternative: A
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
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-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /0/0
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-    dp: 2216
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-  Case_1_mother-N1-DNA1-WGS1:
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-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap
deleted file mode 100644
index 42b81936..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 13611
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 3717
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-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap
deleted file mode 100644
index dce66dd1..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 13928
-reference: G
-alternative: C
-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
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-  Case_1_index-N1-DNA1-WGS1:
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-    dp: 2700
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-  Case_1_mother-N1-DNA1-WGS1:
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-gnomad_exomes_hom: 0
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-inhouse_an: 0
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-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap
deleted file mode 100644
index 264a2925..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap
deleted file mode 100644
index 261174f8..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
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----
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap
deleted file mode 100644
index 12916e48..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
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----
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap
deleted file mode 100644
index 72cf3d51..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap
deleted file mode 100644
index 21ea363c..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 16184
-reference: C
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-ann_fields: []
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap
deleted file mode 100644
index d3c70cf2..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap
+++ /dev/null
@@ -1,155 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41252696
-reference: A
-alternative: T
-ann_fields:
-  - allele:
-      Alt:
-        alternative: T
-    consequences:
-      - intron_variant
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-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
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-        term: Transcript
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-      ord: 442
-      total: 5592
-    protein_pos: ~
-    distance: -798
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-  - allele:
-      Alt:
-        alternative: T
-    consequences:
-      - intron_variant
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-    feature_type:
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-        term: Transcript
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-      - Coding
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-      total: 5451
-    protein_pos: ~
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-  - allele:
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-    feature_type:
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-    feature_id: NM_007299.4
-    feature_biotype:
-      - Coding
-    rank:
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-    hgvs_t: c.442-799T>A
-    hgvs_p: p.?
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-      total: 3696
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-      total: 2100
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-  - allele:
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-    hgvs_p: p.?
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap
deleted file mode 100644
index 36e089af..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap
deleted file mode 100644
index 19bf7f0b..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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-reference: T
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-ann_fields: []
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-  Case_1_father-N1-DNA1-WGS1:
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap
deleted file mode 100644
index 8dbee52a..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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-reference: C
-alternative: T
-ann_fields: []
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-  Case_1_father-N1-DNA1-WGS1:
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\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap
deleted file mode 100644
index e5ffe45e..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap
+++ /dev/null
@@ -1,43 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
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-call_info:
-  Case_1_father-N1-DNA1-WGS1:
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-  Case_1_mother-N1-DNA1-WGS1:
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diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap
deleted file mode 100644
index 0865f189..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap
+++ /dev/null
@@ -1,155 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41252697
-reference: A
-alternative: AT
-ann_fields:
-  - allele:
-      Alt:
-        alternative: AT
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
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-      - Coding
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-  - allele:
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-      - intron_variant
-    putative_impact: MODIFIER
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-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007297.4
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-      - Coding
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-      - intron_variant
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-        term: Transcript
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-  - allele:
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-      - intron_variant
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-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007300.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 23
-    hgvs_t: c.442-801_442-800insA
-    hgvs_p: p.?
-    tx_pos:
-      ord: 555
-      total: 7151
-    cds_pos:
-      ord: 442
-      total: 5655
-    protein_pos: ~
-    distance: -800
-    messages: ~
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /1/1
-    quality: 99
-    dp: 45
-    ad: 45
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /1/0
-    quality: 99
-    dp: 33
-    ad: 17
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /1/0
-    quality: 99
-    dp: 33
-    ad: 11
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap
deleted file mode 100644
index f2959fc6..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap
+++ /dev/null
@@ -1,155 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41252697
-reference: A
-alternative: ATT
-ann_fields:
-  - allele:
-      Alt:
-        alternative: ATT
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007294.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 22
-    hgvs_t: c.442-801_442-800insAA
-    hgvs_p: p.?
-    tx_pos:
-      ord: 555
-      total: 7088
-    cds_pos:
-      ord: 442
-      total: 5592
-    protein_pos: ~
-    distance: -800
-    messages: ~
-  - allele:
-      Alt:
-        alternative: ATT
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007297.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 5
-      total: 21
-    hgvs_t: c.301-801_301-800insAA
-    hgvs_p: p.?
-    tx_pos:
-      ord: 495
-      total: 7028
-    cds_pos:
-      ord: 301
-      total: 5451
-    protein_pos: ~
-    distance: -800
-    messages: ~
-  - allele:
-      Alt:
-        alternative: ATT
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007299.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 21
-    hgvs_t: c.442-801_442-800insAA
-    hgvs_p: p.?
-    tx_pos:
-      ord: 549
-      total: 3696
-    cds_pos:
-      ord: 442
-      total: 2100
-    protein_pos: ~
-    distance: -800
-    messages: ~
-  - allele:
-      Alt:
-        alternative: ATT
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007300.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 23
-    hgvs_t: c.442-801_442-800insAA
-    hgvs_p: p.?
-    tx_pos:
-      ord: 555
-      total: 7151
-    cds_pos:
-      ord: 442
-      total: 5655
-    protein_pos: ~
-    distance: -800
-    messages: ~
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 45
-    ad: 0
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /0/1
-    quality: 99
-    dp: 33
-    ad: 16
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /0/1
-    quality: 99
-    dp: 33
-    ad: 21
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap
deleted file mode 100644
index ad7f4bd7..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap
+++ /dev/null
@@ -1,155 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41254393
-reference: G
-alternative: T
-ann_fields:
-  - allele:
-      Alt:
-        alternative: T
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007294.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 22
-    hgvs_t: c.441+1746C>A
-    hgvs_p: p.?
-    tx_pos:
-      ord: 554
-      total: 7088
-    cds_pos:
-      ord: 441
-      total: 5592
-    protein_pos: ~
-    distance: 1745
-    messages: ~
-  - allele:
-      Alt:
-        alternative: T
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007297.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 5
-      total: 21
-    hgvs_t: c.300+1746C>A
-    hgvs_p: p.?
-    tx_pos:
-      ord: 494
-      total: 7028
-    cds_pos:
-      ord: 300
-      total: 5451
-    protein_pos: ~
-    distance: 1745
-    messages: ~
-  - allele:
-      Alt:
-        alternative: T
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007299.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 21
-    hgvs_t: c.441+1746C>A
-    hgvs_p: p.?
-    tx_pos:
-      ord: 548
-      total: 3696
-    cds_pos:
-      ord: 441
-      total: 2100
-    protein_pos: ~
-    distance: 1745
-    messages: ~
-  - allele:
-      Alt:
-        alternative: T
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007300.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 23
-    hgvs_t: c.441+1746C>A
-    hgvs_p: p.?
-    tx_pos:
-      ord: 554
-      total: 7151
-    cds_pos:
-      ord: 441
-      total: 5655
-    protein_pos: ~
-    distance: 1745
-    messages: ~
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/1
-    quality: 66
-    dp: 37
-    ad: 8
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /./.
-    quality: ~
-    dp: ~
-    ad: ~
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 47
-    dp: 35
-    ad: 3
-    phasing_id: ~
-gnomad_exomes_an: 1936
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 167
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf.snap
deleted file mode 100644
index 1d4c5b06..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf.snap
+++ /dev/null
@@ -1,167 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41249263
-reference: G
-alternative: A
-ann_fields:
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - splice_region_variant
-      - synonymous_variant
-    putative_impact: MODERATE
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007294.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 8
-      total: 23
-    hgvs_t: c.591C>T
-    hgvs_p: p.C197=
-    tx_pos:
-      ord: 704
-      total: 7088
-    cds_pos:
-      ord: 591
-      total: 5592
-    protein_pos:
-      ord: 197
-      total: 1864
-    distance: 44
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - splice_region_variant
-      - synonymous_variant
-    putative_impact: MODERATE
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007297.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 7
-      total: 22
-    hgvs_t: c.450C>T
-    hgvs_p: p.C150=
-    tx_pos:
-      ord: 644
-      total: 7028
-    cds_pos:
-      ord: 450
-      total: 5451
-    protein_pos:
-      ord: 150
-      total: 1817
-    distance: 44
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - splice_region_variant
-      - synonymous_variant
-    putative_impact: MODERATE
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007299.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 8
-      total: 22
-    hgvs_t: c.591C>T
-    hgvs_p: p.C197=
-    tx_pos:
-      ord: 698
-      total: 3696
-    cds_pos:
-      ord: 591
-      total: 2100
-    protein_pos:
-      ord: 197
-      total: 700
-    distance: 44
-    messages: ~
-  - allele:
-      Alt:
-        alternative: A
-    consequences:
-      - splice_region_variant
-      - synonymous_variant
-    putative_impact: MODERATE
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007300.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 8
-      total: 24
-    hgvs_t: c.591C>T
-    hgvs_p: p.C197=
-    tx_pos:
-      ord: 704
-      total: 7151
-    cds_pos:
-      ord: 591
-      total: 5655
-    protein_pos:
-      ord: 197
-      total: 1885
-    distance: 44
-    messages: ~
-call_info:
-  Case_1_father-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 52
-    ad: 0
-    phasing_id: ~
-  Case_1_index-N1-DNA1-WGS1:
-    genotype: /0/0
-    quality: 99
-    dp: 46
-    ad: 0
-    phasing_id: ~
-  Case_1_mother-N1-DNA1-WGS1:
-    genotype: /0/1
-    quality: 99
-    dp: 42
-    ad: 21
-    phasing_id: ~
-gnomad_exomes_an: 31398
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 56
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 251304
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 369
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap
deleted file mode 100644
index 1d9ad79a..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap
+++ /dev/null
@@ -1,31 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: MT
-pos: 750
-reference: A
-alternative: G
-ann_fields: []
-call_info:
-  CASE:
-    genotype: /1/1
-    quality: 99
-    dp: 35
-    ad: 35
-    phasing_id: ~
-gnomad_exomes_an: 0
-gnomad_exomes_hom: 0
-gnomad_exomes_het: 0
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf.snap
deleted file mode 100644
index 1e7c2ff7..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf.snap
+++ /dev/null
@@ -1,143 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&seqvar"
----
-chrom: "17"
-pos: 41256074
-reference: CA
-alternative: C
-ann_fields:
-  - allele:
-      Alt:
-        alternative: C
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007294.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 22
-    hgvs_t: c.441+64delT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 554
-      total: 7088
-    cds_pos:
-      ord: 441
-      total: 5592
-    protein_pos: ~
-    distance: 63
-    messages: ~
-  - allele:
-      Alt:
-        alternative: C
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007297.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 5
-      total: 21
-    hgvs_t: c.300+64delT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 494
-      total: 7028
-    cds_pos:
-      ord: 300
-      total: 5451
-    protein_pos: ~
-    distance: 63
-    messages: ~
-  - allele:
-      Alt:
-        alternative: C
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007299.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 21
-    hgvs_t: c.441+64delT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 548
-      total: 3696
-    cds_pos:
-      ord: 441
-      total: 2100
-    protein_pos: ~
-    distance: 63
-    messages: ~
-  - allele:
-      Alt:
-        alternative: C
-    consequences:
-      - intron_variant
-    putative_impact: MODIFIER
-    gene_symbol: BRCA1
-    gene_id: "HGNC:1100"
-    feature_type:
-      SoTerm:
-        term: Transcript
-    feature_id: NM_007300.4
-    feature_biotype:
-      - Coding
-    rank:
-      ord: 6
-      total: 23
-    hgvs_t: c.441+64delT
-    hgvs_p: p.?
-    tx_pos:
-      ord: 554
-      total: 7151
-    cds_pos:
-      ord: 441
-      total: 5655
-    protein_pos: ~
-    distance: 63
-    messages: ~
-call_info:
-  CASE:
-    genotype: "|1|1"
-    quality: 99
-    dp: 80
-    ad: 80
-    phasing_id: 41256074
-gnomad_exomes_an: 20150
-gnomad_exomes_hom: 2725
-gnomad_exomes_het: 5476
-gnomad_exomes_hemi: 0
-gnomad_genomes_an: 0
-gnomad_genomes_hom: 0
-gnomad_genomes_het: 0
-gnomad_genomes_hemi: 0
-helix_an: 0
-helix_hom: 0
-helix_het: 0
-inhouse_an: 0
-inhouse_hom: 0
-inhouse_het: 0
-inhouse_hemi: 0
\ No newline at end of file
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
deleted file mode 100644
index 30f153aa..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap
+++ /dev/null
@@ -1,97 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&query"
----
-consequences:
-  - chromosome_number_variation
-  - exon_loss_variant
-  - frameshift_variant
-  - rare_amino_acid_variant
-  - splice_acceptor_variant
-  - splice_donor_variant
-  - start_lost
-  - stop_gained
-  - stop_lost
-  - transcript_ablation
-  - 3_prime_UTR_truncation
-  - 5_prime_UTR_truncation
-  - conservative_inframe_deletion
-  - conservative_inframe_insertion
-  - disruptive_inframe_deletion
-  - disruptive_inframe_insertion
-  - missense_variant
-  - regulatory_region_ablation
-  - splice_region_variant
-  - TFBS_ablation
-  - 5_prime_UTR_premature_start_codon_gain_variant
-  - initiator_codon_variant
-  - start_retained
-  - stop_retained_variant
-  - synonymous_variant
-  - 3_prime_UTR_variant
-  - 5_prime_UTR_variant
-  - coding_sequence_variant
-  - conserved_intergenic_variant
-  - conserved_intron_variant
-  - downstream_gene_variant
-  - exon_variant
-  - feature_elongation
-  - feature_truncation
-  - gene_variant
-  - intergenic_variant
-  - intron_variant
-  - mature_miRNA_variant
-  - miRNA
-  - NMD_transcript_variant
-  - non_coding_transcript_exon_variant
-  - non_coding_transcript_intron_variant
-  - regulatory_region_amplification
-  - regulatory_region_variant
-  - TF_binding_site_variant
-  - TFBS_amplification
-  - transcript_amplification
-  - transcript_variant
-  - upstream_gene_variant
-quality: {}
-genotype: {}
-transcripts_coding: true
-transcripts_noncoding: true
-max_exon_dist: ~
-var_type_snv: true
-var_type_indel: true
-var_type_mnv: true
-gene_allowlist: ~
-genomic_regions: ~
-require_in_clinvar: false
-clinvar_include_benign: true
-clinvar_include_pathogenic: true
-clinvar_include_likely_benign: true
-clinvar_include_likely_pathogenic: true
-clinvar_include_uncertain_significance: true
-clinvar_include_conflicting_classifications: true
-gnomad_exomes_enabled: false
-gnomad_exomes_carriers: ~
-gnomad_exomes_heterozygous: ~
-gnomad_exomes_homozygous: ~
-gnomad_exomes_hemizygous: ~
-gnomad_exomes_frequency: ~
-gnomad_genomes_enabled: false
-gnomad_genomes_carriers: ~
-gnomad_genomes_heterozygous: ~
-gnomad_genomes_homozygous: ~
-gnomad_genomes_hemizygous: ~
-gnomad_genomes_frequency: ~
-gnomat_mt_enabled: false
-gnomat_mt_carriers: ~
-gnomat_mt_heteroplasmic: ~
-gnomat_mt_homoplasmic: ~
-gnomat_mt_frequency: ~
-helixmtdb_enabled: false
-helixmtdb_frequency: ~
-helixmtdb_heteroplasmic: ~
-helixmtdb_homoplasmic: ~
-inhouse_enabled: false
-inhouse_carriers: ~
-inhouse_heterozygous: ~
-inhouse_homozygous: ~
-inhouse_hemizygous: ~
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
deleted file mode 100644
index 4129328d..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap
+++ /dev/null
@@ -1,106 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&query"
----
-consequences:
-  - chromosome_number_variation
-  - exon_loss_variant
-  - frameshift_variant
-  - rare_amino_acid_variant
-  - splice_acceptor_variant
-  - splice_donor_variant
-  - start_lost
-  - stop_gained
-  - stop_lost
-  - transcript_ablation
-  - 3_prime_UTR_truncation
-  - 5_prime_UTR_truncation
-  - conservative_inframe_deletion
-  - conservative_inframe_insertion
-  - disruptive_inframe_deletion
-  - disruptive_inframe_insertion
-  - missense_variant
-  - regulatory_region_ablation
-  - splice_region_variant
-  - TFBS_ablation
-  - 5_prime_UTR_premature_start_codon_gain_variant
-  - initiator_codon_variant
-  - start_retained
-  - stop_retained_variant
-  - synonymous_variant
-  - 3_prime_UTR_variant
-  - 5_prime_UTR_variant
-  - coding_sequence_variant
-  - conserved_intergenic_variant
-  - conserved_intron_variant
-  - downstream_gene_variant
-  - exon_variant
-  - feature_elongation
-  - feature_truncation
-  - gene_variant
-  - intergenic_variant
-  - intron_variant
-  - mature_miRNA_variant
-  - miRNA
-  - NMD_transcript_variant
-  - non_coding_transcript_exon_variant
-  - non_coding_transcript_intron_variant
-  - regulatory_region_amplification
-  - regulatory_region_variant
-  - TF_binding_site_variant
-  - TFBS_amplification
-  - transcript_amplification
-  - transcript_variant
-  - upstream_gene_variant
-quality:
-  sample:
-    filter_active: drop-variant
-    dp_het: 10
-    dp_hom: 5
-    gq: 10
-    ab: 0.2
-    ad: 3
-    ad_max: ~
-genotype:
-  sample: het
-transcripts_coding: true
-transcripts_noncoding: true
-max_exon_dist: 100
-var_type_snv: true
-var_type_indel: true
-var_type_mnv: true
-gene_allowlist: ~
-genomic_regions: ~
-require_in_clinvar: false
-clinvar_include_benign: false
-clinvar_include_pathogenic: true
-clinvar_include_likely_benign: false
-clinvar_include_likely_pathogenic: true
-clinvar_include_uncertain_significance: false
-clinvar_include_conflicting_classifications: true
-gnomad_exomes_enabled: true
-gnomad_exomes_carriers: ~
-gnomad_exomes_heterozygous: 20
-gnomad_exomes_homozygous: 0
-gnomad_exomes_hemizygous: ~
-gnomad_exomes_frequency: 0.002
-gnomad_genomes_enabled: true
-gnomad_genomes_carriers: ~
-gnomad_genomes_heterozygous: 4
-gnomad_genomes_homozygous: 0
-gnomad_genomes_hemizygous: ~
-gnomad_genomes_frequency: 0.002
-gnomat_mt_enabled: false
-gnomat_mt_carriers: ~
-gnomat_mt_heteroplasmic: ~
-gnomat_mt_homoplasmic: ~
-gnomat_mt_frequency: ~
-helixmtdb_enabled: true
-helixmtdb_frequency: 0.01
-helixmtdb_heteroplasmic: ~
-helixmtdb_homoplasmic: ~
-inhouse_enabled: true
-inhouse_carriers: 20
-inhouse_heterozygous: ~
-inhouse_homozygous: ~
-inhouse_hemizygous: ~
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
deleted file mode 100644
index b7b4762a..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap
+++ /dev/null
@@ -1,80 +0,0 @@
----
-source: src/seqvars/query/schema.rs
-expression: "&query"
----
-consequences:
-  - 3_prime_UTR_variant
-  - 5_prime_UTR_variant
-  - disruptive_inframe_deletion
-  - disruptive_inframe_insertion
-  - downstream_gene_variant
-  - exon_loss_variant
-  - feature_truncation
-  - frameshift_variant
-  - conservative_inframe_deletion
-  - conservative_inframe_insertion
-  - missense_variant
-  - non_coding_transcript_exon_variant
-  - non_coding_transcript_intron_variant
-  - splice_acceptor_variant
-  - splice_donor_variant
-  - splice_region_variant
-  - start_lost
-  - stop_gained
-  - stop_lost
-  - stop_retained_variant
-  - synonymous_variant
-  - transcript_ablation
-  - upstream_gene_variant
-quality:
-  sample:
-    filter_active: drop-variant
-    dp_het: 10
-    dp_hom: 5
-    gq: 10
-    ab: 0.2
-    ad: 3
-    ad_max: ~
-genotype:
-  sample: het
-transcripts_coding: true
-transcripts_noncoding: true
-max_exon_dist: 100
-var_type_snv: true
-var_type_indel: true
-var_type_mnv: true
-gene_allowlist: []
-genomic_regions: ~
-require_in_clinvar: false
-clinvar_include_benign: false
-clinvar_include_pathogenic: true
-clinvar_include_likely_benign: false
-clinvar_include_likely_pathogenic: true
-clinvar_include_uncertain_significance: false
-clinvar_include_conflicting_classifications: true
-gnomad_exomes_enabled: true
-gnomad_exomes_carriers: ~
-gnomad_exomes_heterozygous: 20
-gnomad_exomes_homozygous: 0
-gnomad_exomes_hemizygous: ~
-gnomad_exomes_frequency: 0.002
-gnomad_genomes_enabled: true
-gnomad_genomes_carriers: ~
-gnomad_genomes_heterozygous: 4
-gnomad_genomes_homozygous: 0
-gnomad_genomes_hemizygous: ~
-gnomad_genomes_frequency: 0.002
-gnomat_mt_enabled: false
-gnomat_mt_carriers: ~
-gnomat_mt_heteroplasmic: ~
-gnomat_mt_homoplasmic: ~
-gnomat_mt_frequency: ~
-helixmtdb_enabled: true
-helixmtdb_frequency: 0.01
-helixmtdb_heteroplasmic: ~
-helixmtdb_homoplasmic: ~
-inhouse_enabled: true
-inhouse_carriers: 20
-inhouse_heterozygous: ~
-inhouse_homozygous: ~
-inhouse_hemizygous: ~
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf.snap
deleted file mode 100644
index 94e6a007..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf.snap
+++ /dev/null
@@ -1,64 +0,0 @@
----
-source: src/seqvars/query/mod.rs
-expression: "std::fs::read_to_string(args.path_output.as_str())?"
----
-sodar_uuid	release	chromosome	chromosome_no	reference	alternative	bin	start	end	smallvariantqueryresultset_id	payload
-a2242722-6377-cc86-7d51-ad3f130af08a	GRCh37	17	17	G	A	899	41249263	41249263	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","gene_related":{"identity":{"hgnc_id":"HGNC:1100","hgnc_symbol":"BRCA1"},"consequences":{"hgvs_t":"c.591C>T","hgvs_p":"p.C197=","consequences":["splice_region_variant","synonymous_variant"]},"phenotype":{"is_acmg_sf":true,"is_disease_gene":true},"constraints":{"gnomad_mis_z":2.3217,"gnomad_oe_lof":0.76716,"gnomad_oe_lof_lower":0.666,"gnomad_oe_lof_upper":0.885,"gnomad_oe_mis":0.86592,"gnomad_oe_mis_lower":0.833,"gnomad_oe_mis_upper":0.899,"gnomad_pli":1.4282e-34,"gnomad_syn_z":2.6589}},"variant_related":{"precomputed_scores":{"PHRED":17.97,"spliceai":0.13,"spliceai_argmax":"SpliceAI-don-loss"},"db_ids":{"dbsnp_rs":"rs1799965"},"clinvar":{"vcv":"VCV000055642.108","germline_significance_description":"Benign","germline_review_status":"AGGREGATE_GERMLINE_REVIEW_STATUS_REVIEWED_BY_EXPERT_PANEL"},"frequency":{"gnomad_mtdna":{"allele_freq":0.0014683411,"allele_count":251304,"het_carriers":369,"hom_carriers":0}}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":52,"ad":0,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":46,"ad":0,"gq":99,"gt":"0/0"},"Case_1_mother-N1-DNA1-WGS1":{"dp":42,"ad":21,"gq":99,"gt":"0/1"}}}}
-d13451de-7160-efa2-b230-76fd782de967	GRCh37	17	17	T	C	899	41252332	41252332	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","gene_related":{"identity":{"hgnc_id":"HGNC:1100","hgnc_symbol":"BRCA1"},"consequences":{"hgvs_t":"c.442-435A>G","hgvs_p":"p.?","consequences":["intron_variant"]},"phenotype":{"is_acmg_sf":true,"is_disease_gene":true},"constraints":{"gnomad_mis_z":2.3217,"gnomad_oe_lof":0.76716,"gnomad_oe_lof_lower":0.666,"gnomad_oe_lof_upper":0.885,"gnomad_oe_mis":0.86592,"gnomad_oe_mis_lower":0.833,"gnomad_oe_mis_upper":0.899,"gnomad_pli":1.4282e-34,"gnomad_syn_z":2.6589}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":25,"ad":0,"gq":75,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":28,"ad":14,"gq":99,"gt":"0/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":40,"ad":21,"gq":99,"gt":"0/1"}}}}
-ea9f11f8-dfb0-ca08-a881-0f9ea39c3a6a	GRCh37	17	17	ATATAAT	A	899	41252691	41252697	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","gene_related":{"identity":{"hgnc_id":"HGNC:1100","hgnc_symbol":"BRCA1"},"consequences":{"hgvs_t":"c.442-800_442-795delATTATA","hgvs_p":"p.?","consequences":["intron_variant"]},"phenotype":{"is_acmg_sf":true,"is_disease_gene":true},"constraints":{"gnomad_mis_z":2.3217,"gnomad_oe_lof":0.76716,"gnomad_oe_lof_lower":0.666,"gnomad_oe_lof_upper":0.885,"gnomad_oe_mis":0.86592,"gnomad_oe_mis_lower":0.833,"gnomad_oe_mis_upper":0.899,"gnomad_pli":1.4282e-34,"gnomad_syn_z":2.6589}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":9,"ad":0,"gq":27,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":14,"ad":10,"gq":99,"gt":"0/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":23,"ad":11,"gq":99,"gt":"0/1"}}}}
-fb780859-e8d8-c7bc-37b7-8e2f9b8d68d9	GRCh37	17	17	ATAAT	A	899	41252693	41252697	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","gene_related":{"identity":{"hgnc_id":"HGNC:1100","hgnc_symbol":"BRCA1"},"consequences":{"hgvs_t":"c.442-800_442-797delATTA","hgvs_p":"p.?","consequences":["intron_variant"]},"phenotype":{"is_acmg_sf":true,"is_disease_gene":true},"constraints":{"gnomad_mis_z":2.3217,"gnomad_oe_lof":0.76716,"gnomad_oe_lof_lower":0.666,"gnomad_oe_lof_upper":0.885,"gnomad_oe_mis":0.86592,"gnomad_oe_mis_lower":0.833,"gnomad_oe_mis_upper":0.899,"gnomad_pli":1.4282e-34,"gnomad_syn_z":2.6589}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":9,"ad":0,"gq":27,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":14,"ad":0,"gq":42,"gt":"0/0"},"Case_1_mother-N1-DNA1-WGS1":{"dp":22,"ad":11,"gq":99,"gt":"0/1"}}}}
-5e831ca1-477e-9b21-1e3a-ba7a1f21d500	GRCh37	17	17	A	AT	899	41252697	41252697	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","gene_related":{"identity":{"hgnc_id":"HGNC:1100","hgnc_symbol":"BRCA1"},"consequences":{"hgvs_t":"c.442-801_442-800insA","hgvs_p":"p.?","consequences":["intron_variant"]},"phenotype":{"is_acmg_sf":true,"is_disease_gene":true},"constraints":{"gnomad_mis_z":2.3217,"gnomad_oe_lof":0.76716,"gnomad_oe_lof_lower":0.666,"gnomad_oe_lof_upper":0.885,"gnomad_oe_mis":0.86592,"gnomad_oe_mis_lower":0.833,"gnomad_oe_mis_upper":0.899,"gnomad_pli":1.4282e-34,"gnomad_syn_z":2.6589}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":45,"ad":45,"gq":99,"gt":"1/1"},"Case_1_index-N1-DNA1-WGS1":{"dp":33,"ad":17,"gq":99,"gt":"1/0"},"Case_1_mother-N1-DNA1-WGS1":{"dp":33,"ad":11,"gq":99,"gt":"1/0"}}}}
-37ae6bd2-3910-a1ee-09ac-4e992e019381	GRCh37	17	17	A	ATT	899	41252697	41252697	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","gene_related":{"identity":{"hgnc_id":"HGNC:1100","hgnc_symbol":"BRCA1"},"consequences":{"hgvs_t":"c.442-801_442-800insAA","hgvs_p":"p.?","consequences":["intron_variant"]},"phenotype":{"is_acmg_sf":true,"is_disease_gene":true},"constraints":{"gnomad_mis_z":2.3217,"gnomad_oe_lof":0.76716,"gnomad_oe_lof_lower":0.666,"gnomad_oe_lof_upper":0.885,"gnomad_oe_mis":0.86592,"gnomad_oe_mis_lower":0.833,"gnomad_oe_mis_upper":0.899,"gnomad_pli":1.4282e-34,"gnomad_syn_z":2.6589}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":45,"ad":0,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":33,"ad":16,"gq":99,"gt":"0/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":33,"ad":21,"gq":99,"gt":"0/1"}}}}
-52f6d2dd-4397-0164-da3f-c7b517b61024	GRCh37	17	17	G	T	899	41254393	41254393	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","gene_related":{"identity":{"hgnc_id":"HGNC:1100","hgnc_symbol":"BRCA1"},"consequences":{"hgvs_t":"c.441+1746C>A","hgvs_p":"p.?","consequences":["intron_variant"]},"phenotype":{"is_acmg_sf":true,"is_disease_gene":true},"constraints":{"gnomad_mis_z":2.3217,"gnomad_oe_lof":0.76716,"gnomad_oe_lof_lower":0.666,"gnomad_oe_lof_upper":0.885,"gnomad_oe_mis":0.86592,"gnomad_oe_mis_lower":0.833,"gnomad_oe_mis_upper":0.899,"gnomad_pli":1.4282e-34,"gnomad_syn_z":2.6589}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":37,"ad":8,"gq":66,"gt":"0/1"},"Case_1_index-N1-DNA1-WGS1":{"dp":null,"ad":null,"gq":null,"gt":"./."},"Case_1_mother-N1-DNA1-WGS1":{"dp":35,"ad":3,"gq":47,"gt":"0/0"}}}}
-fcad5acd-80e4-e585-9021-80d1eb16fd37	GRCh37	17	17	C	CA	899	41273700	41273700	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","gene_related":{"identity":{"hgnc_id":"HGNC:1100","hgnc_symbol":"BRCA1"},"consequences":{"hgvs_t":"c.80+2333_80+2334insT","hgvs_p":"p.?","consequences":["intron_variant"]},"phenotype":{"is_acmg_sf":true,"is_disease_gene":true},"constraints":{"gnomad_mis_z":2.3217,"gnomad_oe_lof":0.76716,"gnomad_oe_lof_lower":0.666,"gnomad_oe_lof_upper":0.885,"gnomad_oe_mis":0.86592,"gnomad_oe_mis_lower":0.833,"gnomad_oe_mis_upper":0.899,"gnomad_pli":1.4282e-34,"gnomad_syn_z":2.6589}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":14,"ad":0,"gq":42,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":7,"ad":1,"gq":10,"gt":"0/0"},"Case_1_mother-N1-DNA1-WGS1":{"dp":10,"ad":5,"gq":65,"gt":"0/1"}}}}
-ca2f07a3-7c4b-3903-f3d3-0e29217ced84	GRCh37	MT	25	A	G	585	73	73	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","variant_related":{"clinvar":{"vcv":"VCV003066071.1","germline_significance_description":"Affects","germline_review_status":"AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED"}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":3975,"ad":0,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":2871,"ad":2871,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":3320,"ad":3320,"gq":99,"gt":"1/1"}}}}
-e4565a76-7abc-de0c-1f55-83a9c9c77da5	GRCh37	MT	25	T	C	585	119	119	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":5418,"ad":1,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":4039,"ad":4039,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":4113,"ad":4112,"gq":99,"gt":"1/1"}}}}
-bff5c542-d0b9-85d8-32a8-af76ab056b7f	GRCh37	MT	25	A	G	585	189	189	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":3069,"ad":0,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":1721,"ad":1721,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":2204,"ad":2204,"gq":99,"gt":"1/1"}}}}
-c34f9afa-1bc0-8781-253f-0a6a3f83f90e	GRCh37	MT	25	T	C	585	195	195	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":2599,"ad":0,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":1592,"ad":1592,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1815,"ad":1815,"gq":99,"gt":"1/1"}}}}
-50cbce17-63d8-db59-5238-4e4d1f429372	GRCh37	MT	25	T	C	585	204	204	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":2180,"ad":0,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":1424,"ad":1424,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1304,"ad":1304,"gq":99,"gt":"1/1"}}}}
-d590cf23-b4ce-5ccb-c44f-249531de1a34	GRCh37	MT	25	G	A	585	207	207	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":2115,"ad":0,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":1408,"ad":1408,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1277,"ad":1277,"gq":99,"gt":"1/1"}}}}
-f233ea84-cdaf-d666-d3ab-072afee793a7	GRCh37	MT	25	A	G	585	263	263	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","variant_related":{"clinvar":{"vcv":"VCV000441147.1","germline_significance_description":"not provided","germline_review_status":"AGGREGATE_GERMLINE_REVIEW_STATUS_NO_CLASSIFICATION_PROVIDED"}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":1288,"ad":1288,"gq":99,"gt":"1/1"},"Case_1_index-N1-DNA1-WGS1":{"dp":1204,"ad":1204,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1031,"ad":1031,"gq":99,"gt":"1/1"}}}}
-e1468add-b464-8a6c-ec2e-103200bd73e3	GRCh37	MT	25	T	TC	585	310	310	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":1035,"ad":1035,"gq":99,"gt":"1/1"},"Case_1_index-N1-DNA1-WGS1":{"dp":1411,"ad":1411,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1091,"ad":1090,"gq":99,"gt":"1/1"}}}}
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-a117eee4-5fb5-13e0-a8bf-03d115fd4851	GRCh37	MT	25	G	C	585	13928	13928	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","variant_related":{"clinvar":{"vcv":"VCV000693635.1","germline_significance_description":"Benign","germline_review_status":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":2947,"ad":0,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":2700,"ad":2700,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1880,"ad":1880,"gq":99,"gt":"1/1"}}}}
-f426c9bc-5baf-cc24-1cd4-b4f0c48dd349	GRCh37	MT	25	A	G	585	14148	14148	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","variant_related":{"clinvar":{"vcv":"VCV000235351.2","germline_significance_description":"Likely benign","germline_review_status":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":3021,"ad":2,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":2820,"ad":2820,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1962,"ad":1962,"gq":99,"gt":"1/1"}}}}
-5c5bade4-3c09-99ec-3045-cfea5c41a4bd	GRCh37	MT	25	C	T	585	14766	14766	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","variant_related":{"clinvar":{"vcv":"VCV000140587.4","germline_significance_description":"Benign","germline_review_status":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":3321,"ad":3,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":3113,"ad":3111,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":2358,"ad":2355,"gq":99,"gt":"1/1"}}}}
-fc0ad6a5-9b72-6d44-3f3f-eba9c6063b22	GRCh37	MT	25	A	G	585	15326	15326	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","variant_related":{"clinvar":{"vcv":"VCV000140592.4","germline_significance_description":"Benign","germline_review_status":"AGGREGATE_GERMLINE_REVIEW_STATUS_REVIEWED_BY_EXPERT_PANEL"}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":3716,"ad":3716,"gq":99,"gt":"1/1"},"Case_1_index-N1-DNA1-WGS1":{"dp":3560,"ad":3560,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":2690,"ad":2690,"gq":99,"gt":"1/1"}}}}
-07946d87-b13b-ecd7-5bc0-cbaec6683927	GRCh37	MT	25	G	C	585	15884	15884	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","variant_related":{"clinvar":{"vcv":"VCV000252455.3","germline_significance_description":"Benign","germline_review_status":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":3596,"ad":1,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":3167,"ad":3167,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":2734,"ad":2733,"gq":99,"gt":"1/1"}}}}
-955a08b1-21df-a068-e505-f72fd12bc865	GRCh37	MT	25	C	T	585	16184	16184	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":1407,"ad":1,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":1969,"ad":1969,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1478,"ad":1478,"gq":99,"gt":"1/1"}}}}
-0799c875-65b8-bb96-fb14-b76e309200e2	GRCh37	MT	25	C	T	585	16223	16223	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","variant_related":{"clinvar":{"vcv":"VCV003027423.1","germline_significance_description":"association not found","germline_review_status":"AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED"}},"call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":1406,"ad":1,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":2018,"ad":2018,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1472,"ad":1472,"gq":99,"gt":"1/1"}}}}
-98270734-fa7f-4c24-04fa-7f924e14ee8d	GRCh37	MT	25	T	C	585	16263	16263	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":1478,"ad":1476,"gq":99,"gt":"1/1"},"Case_1_index-N1-DNA1-WGS1":{"dp":1994,"ad":0,"gq":99,"gt":"0/0"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1475,"ad":0,"gq":99,"gt":"0/0"}}}}
-02f0fa52-18be-3379-375e-5fc324e05bc6	GRCh37	MT	25	C	T	585	16292	16292	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":1652,"ad":0,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":1914,"ad":1913,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1476,"ad":1476,"gq":99,"gt":"1/1"}}}}
-bef71ebc-fa2d-758a-cd58-2732175691e4	GRCh37	MT	25	T	C	585	16519	16519	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":1759,"ad":1759,"gq":99,"gt":"1/1"},"Case_1_index-N1-DNA1-WGS1":{"dp":4094,"ad":4094,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1744,"ad":1744,"gq":99,"gt":"1/1"}}}}
diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf.snap
deleted file mode 100644
index 88d846a5..00000000
--- a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf.snap
+++ /dev/null
@@ -1,7 +0,0 @@
----
-source: src/seqvars/query/mod.rs
-expression: "std::fs::read_to_string(args.path_output.as_str())?"
----
-sodar_uuid	release	chromosome	chromosome_no	reference	alternative	bin	start	end	smallvariantqueryresultset_id	payload
-a2242722-6377-cc86-7d51-ad3f130af08a	GRCh37	17	17	CA	C	899	41256074	41256075	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","gene_related":{"identity":{"hgnc_id":"HGNC:1100","hgnc_symbol":"BRCA1"},"consequences":{"hgvs_t":"c.441+64delT","hgvs_p":"p.?","consequences":["intron_variant"]},"phenotype":{"is_acmg_sf":true,"is_disease_gene":true},"constraints":{"gnomad_mis_z":2.3217,"gnomad_oe_lof":0.76716,"gnomad_oe_lof_lower":0.666,"gnomad_oe_lof_upper":0.885,"gnomad_oe_mis":0.86592,"gnomad_oe_mis_lower":0.833,"gnomad_oe_mis_upper":0.899,"gnomad_pli":1.4282e-34,"gnomad_syn_z":2.6589}},"variant_related":{"precomputed_scores":{"PHRED":4.373,"spliceai":0.0,"spliceai_argmax":"SpliceAI-acc-gain"},"db_ids":{"dbsnp_rs":"rs72434991"}},"call_related":{"call_info":{"CASE":{"dp":80,"ad":80,"gq":99,"gt":"1|1"}}}}
-d13451de-7160-efa2-b230-76fd782de967	GRCh37	MT	25	A	G	585	750	750	.	{"case_uuid":"00000000-0000-0000-0000-000000000000","variant_related":{"clinvar":{"vcv":"VCV000441148.2","germline_significance_description":"association not found","germline_review_status":"AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED"}},"call_related":{"call_info":{"CASE":{"dp":35,"ad":35,"gq":99,"gt":"1/1"}}}}
diff --git a/src/seqvars/query/sorting.rs b/src/seqvars/query/sorting.rs
index b1795c23..486907cb 100644
--- a/src/seqvars/query/sorting.rs
+++ b/src/seqvars/query/sorting.rs
@@ -1,16 +1,16 @@
-//! Code for sorting `SequenceVariant` records by HGNC ID or coordinate.
+//! Code for sorting `VariantRecord` records by HGNC ID or coordinate.
 
-use super::schema::SequenceVariant;
+use super::schema::data::VariantRecord;
 
-/// Helper wrapper that allows to sort `SequenceVariant` by HGNC ID.
+/// Helper wrapper that allows to sort `VariantRecord` by HGNC ID.
 #[derive(Debug, serde::Serialize, serde::Deserialize)]
 pub struct ByHgncId {
     pub hgnc_id: String,
-    pub seqvar: SequenceVariant,
+    pub seqvar: VariantRecord,
 }
 
-impl From<SequenceVariant> for ByHgncId {
-    fn from(val: SequenceVariant) -> Self {
+impl From<VariantRecord> for ByHgncId {
+    fn from(val: VariantRecord) -> Self {
         Self {
             hgnc_id: if !val.ann_fields.is_empty() {
                 val.ann_fields[0].gene_id.clone()
@@ -42,17 +42,17 @@ impl Ord for ByHgncId {
     }
 }
 
-/// Helper wrapper that allows to sort `SequenceVariant` by coordinate.
+/// Helper wrapper that allows to sort `VariantRecord` by coordinate.
 #[derive(Debug, serde::Serialize, serde::Deserialize)]
 pub struct ByCoordinate {
     pub coordinate: (String, i32),
-    pub seqvar: SequenceVariant,
+    pub seqvar: VariantRecord,
 }
 
-impl From<SequenceVariant> for ByCoordinate {
-    fn from(val: SequenceVariant) -> Self {
+impl From<VariantRecord> for ByCoordinate {
+    fn from(val: VariantRecord) -> Self {
         Self {
-            coordinate: (val.chrom.clone(), val.pos),
+            coordinate: (val.vcf_variant.chrom.clone(), val.vcf_variant.pos),
             seqvar: val,
         }
     }
diff --git a/src/strucvars/query/mod.rs b/src/strucvars/query/mod.rs
index ec0a0a51..43613a1e 100644
--- a/src/strucvars/query/mod.rs
+++ b/src/strucvars/query/mod.rs
@@ -834,11 +834,8 @@ pub struct InMemoryDbs {
     pub clinvar_sv: ClinvarSv,
 }
 
-/// Translate gene allow list to gene identifier sfrom
-pub fn translate_gene_allowlist(
-    gene_allowlist: &Vec<String>,
-    dbs: &InMemoryDbs,
-) -> HashSet<String> {
+/// Translate gene allow list to gene identifiers from in-memory dbs.
+pub fn translate_genes(genes: &Vec<String>, dbs: &InMemoryDbs) -> HashSet<String> {
     let mut result = HashSet::new();
 
     let re_entrez = regex::Regex::new(r"^\d+").expect("invalid regex in source code");
@@ -855,7 +852,7 @@ pub fn translate_gene_allowlist(
             .map(|record| (record.symbol.clone(), record.hgnc_id.clone())),
     );
 
-    for gene in gene_allowlist {
+    for gene in genes {
         let gene = gene.trim();
         if re_entrez.is_match(gene) {
             if let Ok(gene_id) = numeric_gene_id(gene) {
@@ -986,7 +983,7 @@ pub async fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), a
         if gene_allowlist.is_empty() {
             None
         } else {
-            Some(translate_gene_allowlist(gene_allowlist, &dbs))
+            Some(translate_genes(gene_allowlist, &dbs))
         }
     } else {
         None

From 0745d874d4191b36bef3b910314ed7a3fd765951 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Fri, 2 Aug 2024 15:15:47 +0200
Subject: [PATCH 18/23] wip

---
 src/seqvars/query/annonars.rs                 |  7 +++--
 src/seqvars/query/interpreter/consequences.rs | 17 +++++++++--
 src/seqvars/query/schema/data.rs              | 28 ++++++++---------
 src/seqvars/query/schema/query.rs             | 30 ++++++++++++-------
 4 files changed, 52 insertions(+), 30 deletions(-)

diff --git a/src/seqvars/query/annonars.rs b/src/seqvars/query/annonars.rs
index 2d430c23..bf38f283 100644
--- a/src/seqvars/query/annonars.rs
+++ b/src/seqvars/query/annonars.rs
@@ -175,14 +175,15 @@ impl Annotator {
 
         raw_value
             .map(|raw_value| {
-                annonars::pbs::genes::base::Record::decode(std::io::Cursor::new(raw_value))
-                    .map_err(|e| {
+                annonars::pbs::genes::base::Record::decode(std::io::Cursor::new(raw_value)).map_err(
+                    |e| {
                         anyhow::anyhow!(
                             "problem decoding record from genes database for HGNC ID {}: {}",
                             hgnc_id,
                             e
                         )
-                    })
+                    },
+                )
             })
             .transpose()
     }
diff --git a/src/seqvars/query/interpreter/consequences.rs b/src/seqvars/query/interpreter/consequences.rs
index e939f808..83c60817 100644
--- a/src/seqvars/query/interpreter/consequences.rs
+++ b/src/seqvars/query/interpreter/consequences.rs
@@ -14,9 +14,17 @@ pub fn passes(query: &CaseQuery, seqvar: &VariantRecord) -> Result<bool, anyhow:
         return Ok(true);
     }
 
-    let query_csq: indexmap::IndexSet<ann::Consequence> = indexmap::IndexSet::from_iter(query.consequence.consequences.iter().cloned().map(|c| c.into()));
+    let query_csq: indexmap::IndexSet<ann::Consequence> = indexmap::IndexSet::from_iter(
+        query
+            .consequence
+            .consequences
+            .iter()
+            .cloned()
+            .map(|c| c.into()),
+    );
     for ann_field in &seqvar.ann_fields {
-        let seqvar_csq: indexmap::IndexSet<ann::Consequence> = indexmap::IndexSet::from_iter(ann_field.consequences.iter().cloned());
+        let seqvar_csq: indexmap::IndexSet<ann::Consequence> =
+            indexmap::IndexSet::from_iter(ann_field.consequences.iter().cloned());
         let intersection_csq = query_csq.intersection(&seqvar_csq);
         if intersection_csq.count() > 0 {
             return Ok(true);
@@ -52,7 +60,10 @@ mod test {
             let query = CaseQuery {
                 consequence: QuerySettingsConsequence {
                     consequences: Consequence::iter()
-                        .filter(|c| (<Consequence as Into<ann::Consequence>>::into(*c) == csq) == c_equals_csq)
+                        .filter(|c| {
+                            (<Consequence as Into<ann::Consequence>>::into(*c) == csq)
+                                == c_equals_csq
+                        })
                         .collect(),
                     ..Default::default()
                 },
diff --git a/src/seqvars/query/schema/data.rs b/src/seqvars/query/schema/data.rs
index 2b40e1fa..2a0a1f2f 100644
--- a/src/seqvars/query/schema/data.rs
+++ b/src/seqvars/query/schema/data.rs
@@ -312,13 +312,13 @@ pub struct VcfVariant {
     pub alt_allele: String,
 }
 
-impl Into<annonars::common::spdi::Var> for VcfVariant {
-    fn into(self) -> annonars::common::spdi::Var {
+impl From<VcfVariant> for annonars::common::spdi::Var {
+    fn from(val: VcfVariant) -> Self {
         annonars::common::spdi::Var::new(
-            annonars::common::cli::canonicalize(&self.chrom),
-            self.pos,
-            self.ref_allele,
-            self.alt_allele,
+            annonars::common::cli::canonicalize(&val.chrom),
+            val.pos,
+            val.ref_allele,
+            val.alt_allele,
         )
     }
 }
@@ -384,7 +384,7 @@ pub(crate) mod call_infos {
         #[error("Empty FORMAT/AD")]
         EmptyFormatAd,
         #[error("Problem parsing genotype: {0}")]
-        GenotypeParseError(#[from] GenotypeToStringError),
+        GenotypeParsing(#[from] GenotypeToStringError),
     }
 }
 
@@ -471,7 +471,7 @@ pub(crate) mod ann_fields {
     #[derive(thiserror::Error, Debug, Clone)]
     pub enum Error {
         #[error("Problem parsing INFO/ANN: {0}")]
-        ParseError(String),
+        Parsing(String),
         #[error("Invalid type of INFO/ANN")]
         InvalidTypeInfoAnn,
     }
@@ -495,10 +495,10 @@ impl TryFromVcf for AnnFields {
                         .flatten()
                         .map(|s| s.parse::<mehari::annotate::seqvars::ann::AnnField>())
                         .collect::<Result<Vec<_>, _>>()
-                        .map_err(|e| Self::Error::ParseError(format!("{}", e)))?,
+                        .map_err(|e| Self::Error::Parsing(format!("{}", e)))?,
                 })
             } else {
-                return Err(ann_fields::Error::InvalidTypeInfoAnn);
+                Err(ann_fields::Error::InvalidTypeInfoAnn)
             }
         } else {
             Ok(Default::default())
@@ -525,13 +525,13 @@ pub(crate) mod variant_record {
     #[derive(thiserror::Error, Debug, Clone)]
     pub enum Error {
         #[error("Problem with variant description: {0:?}")]
-        VcfVariantError(#[from] super::vcf_variant::Error),
+        VcfVariant(#[from] super::vcf_variant::Error),
         #[error("Problem with call information: {0:?}")]
-        CallInfosError(#[from] super::call_infos::Error),
+        CallInfos(#[from] super::call_infos::Error),
         #[error("Problem with annotation fields: {0:?}")]
-        AnnFieldsError(#[from] super::ann_fields::Error),
+        AnnFields(#[from] super::ann_fields::Error),
         #[error("Problem with population frequencies: {0:?}")]
-        PopulationFrequenciesError(#[from] super::population_frequencies::Error),
+        PopulationFrequencies(#[from] super::population_frequencies::Error),
     }
 }
 
diff --git a/src/seqvars/query/schema/query.rs b/src/seqvars/query/schema/query.rs
index 065ddce3..609831cb 100644
--- a/src/seqvars/query/schema/query.rs
+++ b/src/seqvars/query/schema/query.rs
@@ -330,7 +330,7 @@ impl TryFrom<pb_query::QuerySettingsGenotype> for QuerySettingsGenotype {
         let mut sample_genotypes = indexmap::IndexMap::new();
         for pb_sample_genotype in value.sample_genotypes {
             let sample_genotype = SampleGenotypeChoice::try_from(pb_sample_genotype)
-                .map_err(|e| Self::Error::InvalidSampleGenotypeChoice(e))?;
+                .map_err(Self::Error::InvalidSampleGenotypeChoice)?;
             if sample_genotypes.contains_key(&sample_genotype.sample) {
                 return Err(Self::Error::DuplicateSample(sample_genotype.sample));
             }
@@ -658,7 +658,17 @@ impl TryFrom<pb_query::TranscriptType> for TranscriptType {
 
 /// Consequence types.
 #[derive(
-    Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash, serde::Serialize, serde::Deserialize, strum::EnumIter
+    Debug,
+    Clone,
+    Copy,
+    PartialEq,
+    Eq,
+    PartialOrd,
+    Ord,
+    Hash,
+    serde::Serialize,
+    serde::Deserialize,
+    strum::EnumIter,
 )]
 pub enum Consequence {
     /*
@@ -819,11 +829,11 @@ impl TryFrom<pb_query::Consequence> for Consequence {
     }
 }
 
-impl Into<mehari::annotate::seqvars::ann::Consequence> for Consequence {
-    fn into(self) -> mehari::annotate::seqvars::ann::Consequence {
+impl From<Consequence> for mehari::annotate::seqvars::ann::Consequence {
+    fn from(val: Consequence) -> Self {
         use mehari::annotate::seqvars::ann;
 
-        match self {
+        match val {
             Consequence::TranscriptAblation => ann::Consequence::TranscriptAblation,
             Consequence::ExonLossVariant => ann::Consequence::ExonLossVariant,
             Consequence::SpliceAcceptorVariant => ann::Consequence::SpliceAcceptorVariant,
@@ -1165,18 +1175,18 @@ impl TryFrom<pb_query::CaseQuery> for CaseQuery {
 
         let genotype =
             QuerySettingsGenotype::try_from(genotype.ok_or(Self::Error::GenotypeMissing)?)
-                .map_err(|e| Self::Error::GenotypeConversion(e))?;
+                .map_err(Self::Error::GenotypeConversion)?;
         let quality = QuerySettingsQuality::try_from(quality.ok_or(Self::Error::QualityMissing)?)
-            .map_err(|e| Self::Error::QualityConversion(e))?;
+            .map_err(Self::Error::QualityConversion)?;
         let frequency =
             QuerySettingsFrequency::try_from(frequency.ok_or(Self::Error::FrequencyMissing)?)
-                .map_err(|e| Self::Error::FrequencyConversion(e))?;
+                .map_err(Self::Error::FrequencyConversion)?;
         let consequence =
             QuerySettingsConsequence::try_from(consequence.ok_or(Self::Error::ConsequenceMissing)?)
-                .map_err(|e| Self::Error::ConsequenceConversion(e))?;
+                .map_err(Self::Error::ConsequenceConversion)?;
         let locus = QuerySettingsLocus::from(locus.ok_or(Self::Error::LocusMissing)?);
         let clinvar = QuerySettingsClinVar::try_from(clinvar.ok_or(Self::Error::ClinVarMissing)?)
-            .map_err(|e| Self::Error::ClinVarConversion(e))?;
+            .map_err(Self::Error::ClinVarConversion)?;
 
         Ok(Self {
             genotype,

From 55f95e9a6dc61196100da482758dbd9f2ebeb0b9 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Fri, 2 Aug 2024 15:19:09 +0200
Subject: [PATCH 19/23] wip

---
 src/seqvars/query/interpreter/genotype.rs |  2 +-
 src/seqvars/query/mod.rs                  |  2 +-
 src/seqvars/query/schema/data.rs          |  2 +-
 src/seqvars/query/schema/query.rs         | 50 ++++++++++-------------
 src/strucvars/txt_to_bin/masked.rs        |  1 +
 src/strucvars/txt_to_bin/vardbs/input.rs  |  6 +++
 6 files changed, 32 insertions(+), 31 deletions(-)

diff --git a/src/seqvars/query/interpreter/genotype.rs b/src/seqvars/query/interpreter/genotype.rs
index 0da62c02..dc1a6213 100644
--- a/src/seqvars/query/interpreter/genotype.rs
+++ b/src/seqvars/query/interpreter/genotype.rs
@@ -41,7 +41,7 @@ fn passes_recessive_modes(
             e
         )
     })?;
-    let parent_names = query_genotype.recessive_parents().map_err(|e| {
+    let _parent_names = query_genotype.recessive_parents().map_err(|e| {
         anyhow::anyhow!(
             "invalid recessive parents in genotype filter {:?}: {}",
             &query_genotype,
diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs
index ff07d96e..e20c31c8 100644
--- a/src/seqvars/query/mod.rs
+++ b/src/seqvars/query/mod.rs
@@ -98,7 +98,7 @@ fn passes_for_gene(query: &CaseQuery, seqvars: &Vec<VariantRecord>) -> Result<bo
         {
             match genotype {
                 GenotypeChoice::RecessiveIndex => {
-                    index = sample_name.clone();
+                    index.clone_from(sample_name);
                 }
                 GenotypeChoice::RecessiveParent => {
                     parents.push(sample_name.clone());
diff --git a/src/seqvars/query/schema/data.rs b/src/seqvars/query/schema/data.rs
index 2a0a1f2f..7a3aa9f5 100644
--- a/src/seqvars/query/schema/data.rs
+++ b/src/seqvars/query/schema/data.rs
@@ -340,7 +340,7 @@ impl TryFromVcf for VcfVariant {
 
     fn try_from_vcf(
         record: &vcf::variant::RecordBuf,
-        header: &vcf::Header,
+        _header: &vcf::Header,
     ) -> Result<Self, Self::Error> {
         let chrom = record.reference_sequence_name().to_string();
         let pos = usize::from(
diff --git a/src/seqvars/query/schema/query.rs b/src/seqvars/query/schema/query.rs
index 609831cb..cec2a4f6 100644
--- a/src/seqvars/query/schema/query.rs
+++ b/src/seqvars/query/schema/query.rs
@@ -544,15 +544,15 @@ pub(crate) mod query_settings_frequency {
     #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
     pub enum Error {
         #[error("gnomad_exomes missing in protobuf")]
-        GnomadExomesMissing,
+        GnomadExomes,
         #[error("gnomad_genomes missing in protobuf")]
-        GnomadGenomesMissing,
+        GnomadGenomes,
         #[error("gnomad_mt missing in protobuf")]
-        GnomadMtMissing,
+        GnomadMt,
         #[error("helixmtdb missing in protobuf")]
-        HelixMtDbMissing,
+        HelixMtDb,
         #[error("inhouse missing in protobuf")]
-        InhouseMissing,
+        Inhouse,
     }
 }
 
@@ -562,24 +562,18 @@ impl TryFrom<pb_query::QuerySettingsFrequency> for QuerySettingsFrequency {
     fn try_from(value: pb_query::QuerySettingsFrequency) -> Result<Self, Self::Error> {
         Ok(Self {
             gnomad_exomes: GnomadNuclearFrequencySettings::from(
-                value
-                    .gnomad_exomes
-                    .ok_or(Self::Error::GnomadExomesMissing)?,
+                value.gnomad_exomes.ok_or(Self::Error::GnomadExomes)?,
             ),
             gnomad_genomes: GnomadNuclearFrequencySettings::from(
-                value
-                    .gnomad_genomes
-                    .ok_or(Self::Error::GnomadGenomesMissing)?,
+                value.gnomad_genomes.ok_or(Self::Error::GnomadGenomes)?,
             ),
             gnomad_mt: GnomadMitochondrialFrequencySettings::from(
-                value.gnomad_mt.ok_or(Self::Error::GnomadMtMissing)?,
+                value.gnomad_mt.ok_or(Self::Error::GnomadMt)?,
             ),
             helixmtdb: HelixMtDbFrequencySettings::from(
-                value.helixmtdb.ok_or(Self::Error::HelixMtDbMissing)?,
-            ),
-            inhouse: InhouseFrequencySettings::from(
-                value.inhouse.ok_or(Self::Error::InhouseMissing)?,
+                value.helixmtdb.ok_or(Self::Error::HelixMtDb)?,
             ),
+            inhouse: InhouseFrequencySettings::from(value.inhouse.ok_or(Self::Error::Inhouse)?),
         })
     }
 }
@@ -901,17 +895,17 @@ pub(crate) mod query_settings_consequence {
     #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
     pub enum Error {
         #[error("Cannot convert i32 into protobuf VariantType: {0}")]
-        UnknownVariantTypeInt(i32),
+        VariantTypeInt(i32),
         #[error("Cannot convert protobuf VariantType: {0:?}")]
-        UnknownVariantTypeValue(super::pb_query::VariantType),
+        VariantTypeValue(super::pb_query::VariantType),
         #[error("Cannot convert i32 into protobuf TranscriptType: {0}")]
-        UnknownTranscriptTypeInt(i32),
+        TranscriptTypeInt(i32),
         #[error("Cannot convert protobuf TranscriptType: {0:?}")]
-        UnknownTranscriptTypeValue(super::pb_query::TranscriptType),
+        TranscriptTypeValue(super::pb_query::TranscriptType),
         #[error("Cannot convert i32 into protobuf Consequence: {0}")]
-        UnknownConsequenceInt(i32),
+        ConsequenceInt(i32),
         #[error("Cannot convert protobuf Consequence: {0:?}")]
-        UnknownConsequenceValue(super::pb_query::Consequence),
+        ConsequenceValue(super::pb_query::Consequence),
     }
 }
 
@@ -924,9 +918,9 @@ impl TryFrom<pb_query::QuerySettingsConsequence> for QuerySettingsConsequence {
             .into_iter()
             .map(|v| {
                 let v = pb_query::VariantType::try_from(v)
-                    .map_err(|_| query_settings_consequence::Error::UnknownVariantTypeInt(v))?;
+                    .map_err(|_| query_settings_consequence::Error::VariantTypeInt(v))?;
                 VariantType::try_from(v)
-                    .map_err(|_| query_settings_consequence::Error::UnknownVariantTypeValue(v))
+                    .map_err(|_| query_settings_consequence::Error::VariantTypeValue(v))
             })
             .collect::<Result<Vec<_>, _>>()?;
         let transcript_types = value
@@ -934,9 +928,9 @@ impl TryFrom<pb_query::QuerySettingsConsequence> for QuerySettingsConsequence {
             .into_iter()
             .map(|v| {
                 let v = pb_query::TranscriptType::try_from(v)
-                    .map_err(|_| query_settings_consequence::Error::UnknownTranscriptTypeInt(v))?;
+                    .map_err(|_| query_settings_consequence::Error::TranscriptTypeInt(v))?;
                 TranscriptType::try_from(v)
-                    .map_err(|_| query_settings_consequence::Error::UnknownTranscriptTypeValue(v))
+                    .map_err(|_| query_settings_consequence::Error::TranscriptTypeValue(v))
             })
             .collect::<Result<Vec<_>, _>>()?;
         let consequences = value
@@ -944,9 +938,9 @@ impl TryFrom<pb_query::QuerySettingsConsequence> for QuerySettingsConsequence {
             .into_iter()
             .map(|v| {
                 let v = pb_query::Consequence::try_from(v)
-                    .map_err(|_| query_settings_consequence::Error::UnknownConsequenceInt(v))?;
+                    .map_err(|_| query_settings_consequence::Error::ConsequenceInt(v))?;
                 Consequence::try_from(v)
-                    .map_err(|_| query_settings_consequence::Error::UnknownConsequenceValue(v))
+                    .map_err(|_| query_settings_consequence::Error::ConsequenceValue(v))
             })
             .collect::<Result<Vec<_>, _>>()?;
         Ok(Self {
diff --git a/src/strucvars/txt_to_bin/masked.rs b/src/strucvars/txt_to_bin/masked.rs
index 907aff88..83dae920 100644
--- a/src/strucvars/txt_to_bin/masked.rs
+++ b/src/strucvars/txt_to_bin/masked.rs
@@ -25,6 +25,7 @@ mod input {
         /// 1-based end position
         pub end: i32,
         /// Masked region label
+        #[allow(dead_code)]
         pub label: String,
     }
 }
diff --git a/src/strucvars/txt_to_bin/vardbs/input.rs b/src/strucvars/txt_to_bin/vardbs/input.rs
index 4971ae28..192c7334 100644
--- a/src/strucvars/txt_to_bin/vardbs/input.rs
+++ b/src/strucvars/txt_to_bin/vardbs/input.rs
@@ -17,6 +17,7 @@ pub struct DbVarRecord {
     /// end position, 0-based
     pub end: i32,
     /// number of overall carriers
+    #[allow(dead_code)]
     pub num_carriers: u32,
     /// type of the SV
     pub sv_type: String,
@@ -114,22 +115,26 @@ pub struct GnomadSv4Record {
     /// The structural vairant type
     pub svtype: String,
     /// Number of male homozygous reference allele carriers.
+    #[allow(dead_code)]
     pub male_n_homref: u32,
     /// Number of male heterozygous alternate allele carriers.
     pub male_n_het: u32,
     /// Number of male homozygous alternate allele carriers.
     pub male_n_homalt: u32,
     /// Number of male hemizygous alternate allele carriers.
+    #[allow(dead_code)]
     pub male_n_hemiref: u32,
     /// Number of male hemizygous reference allele carriers.
     pub male_n_hemialt: u32,
     /// Number of female homozygous reference allele carriers.
+    #[allow(dead_code)]
     pub female_n_homref: u32,
     /// Number of female heterozygous alternate allele carriers.
     pub female_n_het: u32,
     /// Number of female homozygous alternate allele carriers.
     pub female_n_homalt: u32,
     /// Number of samples at this site (CNV only).
+    #[allow(dead_code)]
     pub cnv_n_total: u32,
     /// Number of samples with a CNV at this site (CNV only).
     pub cnv_n_var: u32,
@@ -147,6 +152,7 @@ pub struct GnomadCnv4Record {
     /// The structural vairant type
     pub svtype: String,
     /// Number of samples at this site (passing QC).
+    #[allow(dead_code)]
     pub n_total: u32,
     /// Number of samples with a CNV at this site (passing QC).
     pub n_var: u32,

From 47f81f4a3e4d26b73a3749d2f3d1d925bc8149d7 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Mon, 5 Aug 2024 10:42:01 +0200
Subject: [PATCH 20/23] wip

---
 protos/varfish/v1/seqvars/query.proto         |    8 +-
 src/seqvars/ingest/header.rs                  |    2 +-
 ...d_output_header_37@clair3_glnexus.vcf.snap |    6 +-
 ...@example_dragen.07.021.624.3.10.4.vcf.snap |    7 +-
 ...@example_dragen.07.021.624.3.10.9.vcf.snap |    7 +-
 ...t_header_37@example_gatk_hc.3.7-0.vcf.snap |    7 +-
 ...header_37@example_gatk_hc.4.4.0.0.vcf.snap |    7 +-
 ...d_output_header_38@clair3_glnexus.vcf.snap |    6 +-
 ...@example_dragen.07.021.624.3.10.4.vcf.snap |    7 +-
 ...@example_dragen.07.021.624.3.10.9.vcf.snap |    7 +-
 ...t_header_38@example_gatk_hc.3.7-0.vcf.snap |    7 +-
 ...header_38@example_gatk_hc.4.4.0.0.vcf.snap |    7 +-
 ...test__result_snapshot_test@Case_1_vcf.snap |   26 +-
 ...sult_snapshot_test@NA12878_dragen_vcf.snap |  164 +--
 ...sult_snapshot_test@clair3_glnexus_vcf.snap |    6 +-
 ...@example_dragen_07_021_624_3_10_4_vcf.snap |    8 +-
 ...@example_dragen_07_021_624_3_10_9_vcf.snap |    8 +-
 ...apshot_test@example_gatk_hc_3_7-0_vcf.snap |    8 +-
 ...shot_test@example_gatk_hc_4_4_0_0_vcf.snap |    8 +-
 ...ingest__test__result_snapshot_test_gz.snap | 1113 +++++++--------
 ..._snapshot_test_with_id_map@Case_1_vcf.snap |   26 +-
 ...t_test_with_id_map@NA12878_dragen_vcf.snap |  164 +--
 src/seqvars/prefilter/mod.rs                  |    1 -
 ...s__prefilter__test__single_output_arg.snap |    4 +-
 ...__prefilter__test__single_output_file.snap |    4 +-
 ...rs__prefilter__test__two_output_arg-2.snap |    2 +-
 ...vars__prefilter__test__two_output_arg.snap |    4 +-
 src/seqvars/query/interpreter/frequency.rs    |   86 +-
 src/seqvars/query/interpreter/genotype.rs     | 1227 +++++++++++++----
 src/seqvars/query/interpreter/mod.rs          |   18 +-
 src/seqvars/query/interpreter/quality.rs      |   62 +-
 src/seqvars/query/mod.rs                      |    6 +-
 src/seqvars/query/output/variant_related.rs   |    8 +-
 src/seqvars/query/schema/data.rs              |   14 +-
 src/seqvars/query/schema/query.rs             |  195 ++-
 ...riant_from_vcf@Case_1.ingested.vcf-10.snap |  203 +++
 ...riant_from_vcf@Case_1.ingested.vcf-11.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-12.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-13.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-14.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-15.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-16.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-17.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-18.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-19.snap |   56 +
 ...ariant_from_vcf@Case_1.ingested.vcf-2.snap |  202 +++
 ...riant_from_vcf@Case_1.ingested.vcf-20.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-21.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-22.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-23.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-24.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-25.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-26.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-27.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-28.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-29.snap |   56 +
 ...ariant_from_vcf@Case_1.ingested.vcf-3.snap |  202 +++
 ...riant_from_vcf@Case_1.ingested.vcf-30.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-31.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-32.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-33.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-34.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-35.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-36.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-37.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-38.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-39.snap |   56 +
 ...ariant_from_vcf@Case_1.ingested.vcf-4.snap |  202 +++
 ...riant_from_vcf@Case_1.ingested.vcf-40.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-41.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-42.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-43.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-44.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-45.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-46.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-47.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-48.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-49.snap |   56 +
 ...ariant_from_vcf@Case_1.ingested.vcf-5.snap |  202 +++
 ...riant_from_vcf@Case_1.ingested.vcf-50.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-51.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-52.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-53.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-54.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-55.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-56.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-57.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-58.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-59.snap |   56 +
 ...ariant_from_vcf@Case_1.ingested.vcf-6.snap |  202 +++
 ...riant_from_vcf@Case_1.ingested.vcf-60.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-61.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-62.snap |   56 +
 ...riant_from_vcf@Case_1.ingested.vcf-63.snap |   56 +
 ...ariant_from_vcf@Case_1.ingested.vcf-7.snap |  202 +++
 ...ariant_from_vcf@Case_1.ingested.vcf-8.snap |  202 +++
 ...ariant_from_vcf@Case_1.ingested.vcf-9.snap |  202 +++
 ..._variant_from_vcf@Case_1.ingested.vcf.snap |  217 +++
 ...ariant_from_vcf@dragen.ingested.vcf-2.snap |   42 +
 ..._variant_from_vcf@dragen.ingested.vcf.snap |  188 +++
 tests/seqvars/aggregate/ingest.vcf            |    4 +-
 tests/seqvars/prefilter/ingest.vcf            |    4 +-
 tests/seqvars/query/Case_1.ingested.vcf       |  132 +-
 tests/seqvars/query/dragen.ingested.vcf       |   12 +-
 104 files changed, 7338 insertions(+), 1288 deletions(-)
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@dragen.ingested.vcf.snap

diff --git a/protos/varfish/v1/seqvars/query.proto b/protos/varfish/v1/seqvars/query.proto
index ae7418fc..92ea929e 100644
--- a/protos/varfish/v1/seqvars/query.proto
+++ b/protos/varfish/v1/seqvars/query.proto
@@ -36,8 +36,10 @@ enum GenotypeChoice {
   GENOTYPE_CHOICE_VARIANT = 7;
   // Recessive index.
   GENOTYPE_CHOICE_RECESSIVE_INDEX = 8;
-  // Recessive parent.
-  GENOTYPE_CHOICE_RECESSIVE_PARENT = 9;
+  // Recessive father.
+  GENOTYPE_CHOICE_RECESSIVE_FATHER = 9;
+  // Recessive mother.
+  GENOTYPE_CHOICE_RECESSIVE_MOTHER = 10;
 }
 
 // Genotype choice for one sample.
@@ -145,7 +147,7 @@ message QuerySettingsFrequency {
   // gnomAD-genomes filter
   GnomadNuclearFreqyencySettings gnomad_genomes = 2;
   // gnomAD-MT filter
-  GnomadMitochondrialFrequencySettings gnomad_mt = 3;
+  GnomadMitochondrialFrequencySettings gnomad_mtdna = 3;
   // HelixMtDb filter
   HelixMtDbFrequencySettings helixmtdb = 4;
   // In-house filter
diff --git a/src/seqvars/ingest/header.rs b/src/seqvars/ingest/header.rs
index b6d828ec..ccd7b1a9 100644
--- a/src/seqvars/ingest/header.rs
+++ b/src/seqvars/ingest/header.rs
@@ -355,7 +355,7 @@ pub fn build_output_header(
                 "Functional annotations: 'Allele | Annotation | Annotation_Impact | \
                 Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | \
                 HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | \
-                AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'",
+                AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'",
             ),
         )
         .add_format(key::READ_DEPTHS, Map::<Format>::from(key::READ_DEPTHS))
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@clair3_glnexus.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@clair3_glnexus.vcf.snap
index 024d7163..c4ac39bc 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@clair3_glnexus.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@clair3_glnexus.vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.4.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.4.vcf.snap
index e361e714..c4df7649 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.4.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.4.vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,4 +57,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.4, HW: 07.021.624">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.9.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.9.vcf.snap
index 86221744..d93f27e6 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.9.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.9.vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,4 +57,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.9, HW: 07.021.624">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CASE
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.3.7-0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.3.7-0.vcf.snap
index 96740364..dcb2e779 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.3.7-0.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.3.7-0.vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -57,4 +61,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.4.4.0.0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.4.4.0.0.vcf.snap
index 30195df3..33c03221 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.4.4.0.0.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.4.4.0.0.vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,4 +57,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="4.4.0.0">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CASE
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@clair3_glnexus.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@clair3_glnexus.vcf.snap
index bb020661..cdb1e50b 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@clair3_glnexus.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@clair3_glnexus.vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap
index 41c85afe..3b836aa9 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,4 +57,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.4, HW: 07.021.624">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap
index 83c2f979..f79bee55 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,4 +57,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.9, HW: 07.021.624">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CASE
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap
index 77d94a21..6387a682 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -57,4 +61,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap
index a4528b87..c5d82c93 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,4 +57,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="4.4.0.0">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CASE
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap
index bf45a940..5c5b34f1 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -57,16 +61,16 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-17	41249263	.	G	A	.	.	gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_vcv=VCV000055642.108;clinvar_germline_classification=Benign;ANN=A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/23|c.591C>T|p.C197=|704/7088|591/5592|197/1864|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.C150=|644/7028|450/5451|150/1817|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/22|c.591C>T|p.C197=|610/3682|591/2280|197/760|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.C197=|698/3696|591/2100|197/700|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.C197=|704/7151|591/5655|197/1885|0|	GT:AD:DP:GQ	0/0:52,0:52:99	0/0:46,0:46:99	0/1:21,21:42:99
-17	41252332	.	T	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-435A>G|p.?|555/7088|442/5592||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-435A>G|p.?|461/3682|442/2280||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||435|	GT:AD:DP:GQ	0/0:25,0:25:75	0/1:14,14:28:99	0/1:19,21:40:99
-17	41252691	.	ATATAAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-795delATTATA|p.?|555/7088|442/5592||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795delATTATA|p.?|495/7028|301/5451||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-795delATTATA|p.?|461/3682|442/2280||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795delATTATA|p.?|549/3696|442/2100||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795delATTATA|p.?|555/7151|442/5655||795|	GT:AD:DP:GQ	0/0:9,0:9:27	0/1:4,10:14:99	0/1:12,11:23:99
-17	41252693	.	ATAAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-797delATTA|p.?|555/7088|442/5592||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797delATTA|p.?|495/7028|301/5451||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-797delATTA|p.?|461/3682|442/2280||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797delATTA|p.?|549/3696|442/2100||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797delATTA|p.?|555/7151|442/5655||797|	GT:AD:DP:GQ	0/0:9,0:9:27	0/0:14,0:14:42	0/1:11,11:22:99
-17	41252695	.	AAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-799delAT|p.?|555/7088|442/5592||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799delAT|p.?|495/7028|301/5451||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-799delAT|p.?|461/3682|442/2280||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799delAT|p.?|549/3696|442/2100||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799delAT|p.?|555/7151|442/5655||799|	GT:AD:DP:GQ	0/1:3,6:9:79	0/0:14,0:14:42	0/0:22,0:22:66
-17	41252696	.	A	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-799T>A|p.?|555/7088|442/5592||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-799T>A|p.?|461/3682|442/2280||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||799|	GT:AD:DP:GQ	0/1:6,3:9:78	0/1:10,4:14:98	0/0:22,0:22:67
-17	41252697	.	A	AT	.	.	ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insA|p.?|461/3682|442/2280||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||801|	GT:AD:DP:GQ	1/1:0,45:45:99	1/0:16,17:33:99	1/0:22,11:33:99
-17	41252697	.	A	ATT	.	.	ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insAA|p.?|461/3682|442/2280||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||801|	GT:AD:DP:GQ	0/0:45,0:45:99	0/1:17,16:33:99	0/1:12,21:33:99
-17	41254393	.	G	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1746C>A|p.?|554/7088|441/5592||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1746C>A|p.?|460/3682|441/2280||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||-1746|	GT:AD:DP:GQ	0/1:29,8:37:66	./.:.:.:.	0/0:32,3:35:47
-17	41273700	.	C	CA	.	.	ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||-2334|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||-2334|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2333_80+2334insT|p.?|99/3682|80/2280||-2334|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||-2334|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||-2334|	GT:AD:DP:GQ	0/0:14,0:14:42	0/0:6,1:7:10	0/1:5,5:10:65
+17	41249263	.	G	A	.	.	gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_vcv=VCV000055642.108;clinvar_germline_classification=Benign;ANN=A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/23|c.591C>T|p.Cys197=|704/7088|591/5592|197/1864|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.Cys150=|644/7028|450/5451|150/1817|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/22|c.591C>T|p.Cys197=|610/3682|591/2280|197/760|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.Cys197=|698/3696|591/2100|197/700|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.Cys197=|704/7151|591/5655|197/1885|0|-1|	GT:AD:DP:GQ	0/0:52,0:52:99	0/0:46,0:46:99	0/1:21,21:42:99
+17	41252332	.	T	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-435A>G|p.?|555/7088|442/5592||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-435A>G|p.?|461/3682|442/2280||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||435|-1|	GT:AD:DP:GQ	0/0:25,0:25:75	0/1:14,14:28:99	0/1:19,21:40:99
+17	41252691	.	ATATAAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-795del|p.?|555/7088|442/5592||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795del|p.?|495/7028|301/5451||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-795del|p.?|461/3682|442/2280||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795del|p.?|549/3696|442/2100||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795del|p.?|555/7151|442/5655||795|-1|	GT:AD:DP:GQ	0/0:9,0:9:27	0/1:4,10:14:99	0/1:12,11:23:99
+17	41252693	.	ATAAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-797del|p.?|555/7088|442/5592||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797del|p.?|495/7028|301/5451||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-797del|p.?|461/3682|442/2280||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797del|p.?|549/3696|442/2100||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797del|p.?|555/7151|442/5655||797|-1|	GT:AD:DP:GQ	0/0:9,0:9:27	0/0:14,0:14:42	0/1:11,11:22:99
+17	41252695	.	AAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-799del|p.?|555/7088|442/5592||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799del|p.?|495/7028|301/5451||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-799del|p.?|461/3682|442/2280||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799del|p.?|549/3696|442/2100||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799del|p.?|555/7151|442/5655||799|-1|	GT:AD:DP:GQ	0/1:3,6:9:79	0/0:14,0:14:42	0/0:22,0:22:66
+17	41252696	.	A	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-799T>A|p.?|555/7088|442/5592||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-799T>A|p.?|461/3682|442/2280||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||799|-1|	GT:AD:DP:GQ	0/1:6,3:9:78	0/1:10,4:14:98	0/0:22,0:22:67
+17	41252697	.	A	AT	.	.	ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insA|p.?|461/3682|442/2280||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||801|-1|	GT:AD:DP:GQ	1/1:0,45:45:99	1/0:16,17:33:99	1/0:22,11:33:99
+17	41252697	.	A	ATT	.	.	ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insAA|p.?|461/3682|442/2280||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||801|-1|	GT:AD:DP:GQ	0/0:45,0:45:99	0/1:17,16:33:99	0/1:12,21:33:99
+17	41254393	.	G	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1746C>A|p.?|554/7088|441/5592||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1746C>A|p.?|460/3682|441/2280||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||-1746|-1|	GT:AD:DP:GQ	0/1:29,8:37:66	./.:.:.:.	0/0:32,3:35:47
+17	41273700	.	C	CA	.	.	ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||-2334|-1|,CA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||-2334|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2333_80+2334insT|p.?|99/3682|80/2280||-2334|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||-2334|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||-2334|-1|	GT:AD:DP:GQ	0/0:14,0:14:42	0/0:6,1:7:10	0/1:5,5:10:65
 MT	73	.	A	G	.	.	clinvar_vcv=VCV003066071.1;clinvar_germline_classification=Affects	GT:AD:DP:GQ	0/0:3975,0:3975:99	1/1:0,2871:2871:99	1/1:0,3320:3320:99
 MT	119	.	T	C	.	.	.	GT:AD:DP:GQ	0/0:5417,1:5418:99	1/1:0,4039:4039:99	1/1:1,4112:4113:99
 MT	189	.	A	G	.	.	.	GT:AD:DP:GQ	0/0:3069,0:3069:99	1/1:0,1721:1721:99	1/1:0,2204:2204:99
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap
index 0bd7b175..bb2baa5c 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,85 +57,85 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.4, HW: 07.021.624">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-17	41244000	.	T	C	.	.	gnomad_exomes_an=31346;gnomad_exomes_hom=1591;gnomad_exomes_het=6707;gnomad_genomes_an=250954;gnomad_genomes_hom=16402;gnomad_genomes_het=55703;clinvar_vcv=VCV000041818.87;clinvar_germline_classification=Benign;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.3548A>G|p.K1183R|3661/7088|3548/5592|1183/1864|0|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.3407A>G|p.K1136R|3601/7028|3407/5451|1136/1817|0|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.788-951A>G|p.?|807/3682|788/2280||951|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-951A>G|p.?|895/3696|788/2100||951|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3548A>G|p.K1183R|3661/7151|3548/5655|1183/1885|0|	GT:AD:DP:GQ	0/1:8,18:26:43
-17	41244435	.	T	C	.	.	gnomad_exomes_an=31332;gnomad_exomes_hom=1505;gnomad_exomes_het=6415;gnomad_genomes_an=251032;gnomad_genomes_hom=16145;gnomad_genomes_het=55137;clinvar_vcv=VCV000041815.87;clinvar_germline_classification=Benign;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.3113A>G|p.E1038G|3226/7088|3113/5592|1038/1864|0|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2972A>G|p.E991G|3166/7028|2972/5451|991/1817|0|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.788-1386A>G|p.?|807/3682|788/2280||1386|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-1386A>G|p.?|895/3696|788/2100||1386|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3113A>G|p.E1038G|3226/7151|3113/5655|1038/1885|0|	GT:AD:DP:GQ	0/1:12,14:26:47
-17	41244936	.	G	A	.	.	gnomad_exomes_an=31324;gnomad_exomes_hom=4287;gnomad_exomes_het=6594;gnomad_genomes_an=251034;gnomad_genomes_hom=22738;gnomad_genomes_het=55898;clinvar_vcv=VCV000041812.88;clinvar_germline_classification=Benign;ANN=A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2612C>T|p.P871L|2725/7088|2612/5592|871/1864|0|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2471C>T|p.P824L|2665/7028|2471/5451|824/1817|0|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1825C>T|p.?|806/3682|787/2280||-1825|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1825C>T|p.?|894/3696|787/2100||-1825|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2612C>T|p.P871L|2725/7151|2612/5655|871/1885|0|	GT:AD:DP:GQ	0/1:17,13:30:47
-17	41245237	.	A	G	.	.	gnomad_exomes_an=31314;gnomad_exomes_hom=1492;gnomad_exomes_het=6416;gnomad_genomes_an=250946;gnomad_genomes_hom=16057;gnomad_genomes_het=55063;clinvar_vcv=VCV000125554.83;clinvar_germline_classification=Benign;ANN=G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2311T>C|p.L771=|2424/7088|2311/5592|771/1864|0|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2170T>C|p.L724=|2364/7028|2170/5451|724/1817|0|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1524T>C|p.?|806/3682|787/2280||-1524|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1524T>C|p.?|894/3696|787/2100||-1524|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2311T>C|p.L771=|2424/7151|2311/5655|771/1885|0|	GT:AD:DP:GQ	0/1:18,11:29:46
-17	41245466	.	G	A	.	.	gnomad_exomes_an=31338;gnomad_exomes_hom=1602;gnomad_exomes_het=6709;gnomad_genomes_an=251110;gnomad_genomes_hom=16420;gnomad_genomes_het=55707;clinvar_vcv=VCV000125536.84;clinvar_germline_classification=Benign;ANN=A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2082C>T|p.S694=|2195/7088|2082/5592|694/1864|0|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.1941C>T|p.S647=|2135/7028|1941/5451|647/1817|0|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1295C>T|p.?|806/3682|787/2280||-1295|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1295C>T|p.?|894/3696|787/2100||-1295|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2082C>T|p.S694=|2195/7151|2082/5655|694/1885|0|	GT:AD:DP:GQ	0/1:11,8:19:48
-17	41247122	.	A	ACCT	.	.	clinvar_vcv=VCV000127125.5;clinvar_germline_classification=Benign;ANN=ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|9/22|c.671-246_671-245insAGG|p.?|784/7088|671/5592||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.530-246_530-245insAGG|p.?|724/7028|530/5451||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|8/21|c.671-246_671-245insAGG|p.?|690/3682|671/2280||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.671-246_671-245insAGG|p.?|778/3696|671/2100||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.671-246_671-245insAGG|p.?|784/7151|671/5655||246|	GT:AD:DP:GQ	0/1:18,11:29:45
-17	41247604	.	A	C	.	.	clinvar_vcv=VCV000209447.5;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|9/22|c.670+259T>G|p.?|783/7088|670/5592||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.529+259T>G|p.?|723/7028|529/5451||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|8/21|c.670+259T>G|p.?|689/3682|670/2280||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.670+259T>G|p.?|777/3696|670/2100||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.670+259T>G|p.?|783/7151|670/5655||-259|	GT:AD:DP:GQ	0/1:12,11:23:47
-17	41248164	.	C	T	.	.	clinvar_vcv=VCV000209449.4;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-225G>A|p.?|707/7088|594/5592||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-225G>A|p.?|647/7028|453/5451||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-225G>A|p.?|613/3682|594/2280||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-225G>A|p.?|701/3696|594/2100||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-225G>A|p.?|707/7151|594/5655||225|	GT:AD:DP:GQ	0/1:14,7:21:44
-17	41248393	.	C	CAAAAAAAAAA	.	.	ANN=CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-455_594-454insTTTTTTTTTT|p.?|707/7088|594/5592||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-455_453-454insTTTTTTTTTT|p.?|647/7028|453/5451||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-455_594-454insTTTTTTTTTT|p.?|613/3682|594/2280||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-455_594-454insTTTTTTTTTT|p.?|701/3696|594/2100||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-455_594-454insTTTTTTTTTT|p.?|707/7151|594/5655||455|	GT:AD:DP:GQ	0/1:9,7:16:48
-17	41248484	.	G	C	.	.	clinvar_vcv=VCV000209450.4;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-545C>G|p.?|707/7088|594/5592||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-545C>G|p.?|647/7028|453/5451||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-545C>G|p.?|613/3682|594/2280||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-545C>G|p.?|701/3696|594/2100||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-545C>G|p.?|707/7151|594/5655||545|	GT:AD:DP:GQ	0/1:11,9:20:48
-17	41248588	.	CA	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-650delT|p.?|707/7088|594/5592||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-650delT|p.?|647/7028|453/5451||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-650delT|p.?|613/3682|594/2280||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-650delT|p.?|701/3696|594/2100||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-650delT|p.?|707/7151|594/5655||650|	GT:AD:DP:GQ	0/1:9,10:19:42
-17	41249094	.	A	G	.	.	gnomad_exomes_an=31332;gnomad_exomes_hom=1602;gnomad_exomes_het=6703;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000209451.5;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.593+167T>C|p.?|706/7088|593/5592||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.452+167T>C|p.?|646/7028|452/5451||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.593+167T>C|p.?|612/3682|593/2280||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.593+167T>C|p.?|700/3696|593/2100||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.593+167T>C|p.?|706/7151|593/5655||-167|	GT:AD:DP:GQ	0/1:9,7:16:48
-17	41249363	.	TA	T	.	.	gnomad_exomes_an=31286;gnomad_exomes_hom=1497;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.548-58delT|p.?|661/7088|548/5592||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-58delT|p.?|601/7028|407/5451||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.548-58delT|p.?|567/3682|548/2280||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-58delT|p.?|655/3696|548/2100||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-58delT|p.?|661/7151|548/5655||58|	GT:AD:DP:GQ	0/1:12,13:25:48
-17	41250047	.	C	CT	.	.	ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.548-742_548-741insA|p.?|661/7088|548/5592||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-742_407-741insA|p.?|601/7028|407/5451||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.548-742_548-741insA|p.?|567/3682|548/2280||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-742_548-741insA|p.?|655/3696|548/2100||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-742_548-741insA|p.?|661/7151|548/5655||742|	GT:AD:DP:GQ	0/1:13,7:20:18
-17	41250678	.	C	CT	.	.	clinvar_vcv=VCV000209458.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+1113_547+1114insA|p.?|660/7088|547/5592||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+1113_406+1114insA|p.?|600/7028|406/5451||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+1113_547+1114insA|p.?|566/3682|547/2280||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+1113_547+1114insA|p.?|654/3696|547/2100||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+1113_547+1114insA|p.?|660/7151|547/5655||-1114|	GT:AD:DP:GQ	0/1:6,16:22:42
-17	41250923	.	T	C	.	.	clinvar_vcv=VCV000209460.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+869A>G|p.?|660/7088|547/5592||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+869A>G|p.?|600/7028|406/5451||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+869A>G|p.?|566/3682|547/2280||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+869A>G|p.?|654/3696|547/2100||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+869A>G|p.?|660/7151|547/5655||-869|	GT:AD:DP:GQ	0/1:13,9:22:47
-17	41251495	.	C	G	.	.	clinvar_vcv=VCV000209463.4;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+297G>C|p.?|660/7088|547/5592||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+297G>C|p.?|600/7028|406/5451||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+297G>C|p.?|566/3682|547/2280||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+297G>C|p.?|654/3696|547/2100||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+297G>C|p.?|660/7151|547/5655||-297|	GT:AD:DP:GQ	0/1:11,15:26:48
-17	41251646	.	T	A	.	.	gnomad_exomes_an=31294;gnomad_exomes_hom=1592;gnomad_exomes_het=6693;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125879.7;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+146A>T|p.?|660/7088|547/5592||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+146A>T|p.?|600/7028|406/5451||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+146A>T|p.?|566/3682|547/2280||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+146A>T|p.?|654/3696|547/2100||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+146A>T|p.?|660/7151|547/5655||-146|	GT:AD:DP:GQ	0/1:11,8:19:48
-17	41252575	.	G	A	.	.	clinvar_vcv=VCV000209466.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-678C>T|p.?|555/7088|442/5592||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-678C>T|p.?|495/7028|301/5451||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-678C>T|p.?|461/3682|442/2280||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-678C>T|p.?|549/3696|442/2100||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-678C>T|p.?|555/7151|442/5655||678|	GT:AD:DP:GQ:PS	1|1:0,3:3:5:41252575
-17	41252591	.	C	CAT	.	.	clinvar_vcv=VCV000264796.2;clinvar_germline_classification=Benign;ANN=CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-695_442-694insAT|p.?|555/7088|442/5592||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-695_301-694insAT|p.?|495/7028|301/5451||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-695_442-694insAT|p.?|461/3682|442/2280||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-695_442-694insAT|p.?|549/3696|442/2100||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-695_442-694insAT|p.?|555/7151|442/5655||695|	GT:AD:DP:GQ:PS	1|1:0,2:2:4:41252575
-17	41254174	.	A	G	.	.	clinvar_vcv=VCV000209478.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1965T>C|p.?|554/7088|441/5592||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1965T>C|p.?|494/7028|300/5451||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1965T>C|p.?|460/3682|441/2280||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1965T>C|p.?|548/3696|441/2100||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1965T>C|p.?|554/7151|441/5655||-1965|	GT:AD:DP:GQ	0/1:14,13:27:48
-17	41254374	.	C	CTTTTTTTT	.	.	ANN=CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1764_441+1765insAAAAAAAA|p.?|554/7088|441/5592||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1764_300+1765insAAAAAAAA|p.?|494/7028|300/5451||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1764_441+1765insAAAAAAAA|p.?|460/3682|441/2280||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1764_441+1765insAAAAAAAA|p.?|548/3696|441/2100||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1764_441+1765insAAAAAAAA|p.?|554/7151|441/5655||-1765|	GT:AD:DP:GQ	0/1:6,7:13:48
-17	41254405	.	C	T	.	.	clinvar_vcv=VCV000264778.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1734G>A|p.?|554/7088|441/5592||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1734G>A|p.?|494/7028|300/5451||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1734G>A|p.?|460/3682|441/2280||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1734G>A|p.?|548/3696|441/2100||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1734G>A|p.?|554/7151|441/5655||-1734|	GT:AD:DP:GQ	0/1:5,9:14:43
-17	41254486	.	T	G	.	.	clinvar_vcv=VCV000209479.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1653A>C|p.?|554/7088|441/5592||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1653A>C|p.?|494/7028|300/5451||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1653A>C|p.?|460/3682|441/2280||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1653A>C|p.?|548/3696|441/2100||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1653A>C|p.?|554/7151|441/5655||-1653|	GT:AD:DP:GQ	0/1:8,15:23:46
-17	41254965	.	C	CT	.	.	clinvar_vcv=VCV000264845.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1173_441+1174insA|p.?|554/7088|441/5592||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1173_300+1174insA|p.?|494/7028|300/5451||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1173_441+1174insA|p.?|460/3682|441/2280||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1173_441+1174insA|p.?|548/3696|441/2100||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1173_441+1174insA|p.?|554/7151|441/5655||-1174|	GT:AD:DP:GQ	0/1:14,8:22:22
-17	41255102	.	A	G	.	.	clinvar_vcv=VCV000209483.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1037T>C|p.?|554/7088|441/5592||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1037T>C|p.?|494/7028|300/5451||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1037T>C|p.?|460/3682|441/2280||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1037T>C|p.?|548/3696|441/2100||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1037T>C|p.?|554/7151|441/5655||-1037|	GT:AD:DP:GQ:PS	0|1:19,12:31:46:41255102
-17	41255111	.	A	T	.	.	clinvar_vcv=VCV000209484.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1028T>A|p.?|554/7088|441/5592||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1028T>A|p.?|494/7028|300/5451||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1028T>A|p.?|460/3682|441/2280||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1028T>A|p.?|548/3696|441/2100||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1028T>A|p.?|554/7151|441/5655||-1028|	GT:AD:DP:GQ:PS	0|1:19,12:31:46:41255102
-17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64delT|p.?|554/7088|441/5592||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64delT|p.?|460/3682|441/2280||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||-64|	GT:AD:DP:GQ:PS	0|1:11,6:17:43:41256074
-17	41256089	.	AAAAAAAAAGAAAAG	A	.	.	gnomad_exomes_an=28388;gnomad_exomes_hom=1079;gnomad_exomes_het=5744;gnomad_genomes_an=167932;gnomad_genomes_hom=9911;gnomad_genomes_het=23697;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7088|441/5592||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+36_300+49delCTTTTCTTTTTTTT|p.?|494/7028|300/5451||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|460/3682|441/2280||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|548/3696|441/2100||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7151|441/5655||-36|	GT:AD:DP:GQ:PS	0|1:13,6:19:43:41256074
-17	41257134	.	T	C	.	.	gnomad_exomes_an=31346;gnomad_exomes_hom=4418;gnomad_exomes_het=6505;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125614.7;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.213-161A>G|p.?|326/7088|213/5592||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-161A>G|p.?|266/7028|72/5451||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.213-161A>G|p.?|232/3682|213/2280||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-161A>G|p.?|320/3696|213/2100||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-161A>G|p.?|326/7151|213/5655||161|	GT:AD:DP:GQ	0/1:14,15:29:48
-17	41257458	.	A	C	.	.	clinvar_vcv=VCV000209489.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.213-485T>G|p.?|326/7088|213/5592||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-485T>G|p.?|266/7028|72/5451||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.213-485T>G|p.?|232/3682|213/2280||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-485T>G|p.?|320/3696|213/2100||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-485T>G|p.?|326/7151|213/5655||485|	GT:AD:DP:GQ	0/1:11,15:26:48
-17	41258043	.	C	T	.	.	clinvar_vcv=VCV000209491.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.212+430G>A|p.?|325/7088|212/5592||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+430G>A|p.?|265/7028|71/5451||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.212+430G>A|p.?|231/3682|212/2280||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+430G>A|p.?|319/3696|212/2100||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+430G>A|p.?|325/7151|212/5655||-430|	GT:AD:DP:GQ	0/1:14,13:27:48
-17	41258135	.	T	TA	.	.	ANN=TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.212+337_212+338insT|p.?|325/7088|212/5592||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+337_71+338insT|p.?|265/7028|71/5451||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.212+337_212+338insT|p.?|231/3682|212/2280||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+337_212+338insT|p.?|319/3696|212/2100||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+337_212+338insT|p.?|325/7151|212/5655||-338|	GT:AD:DP:GQ	1/1:3,11:14:4
-17	41259049	.	C	T	.	.	clinvar_vcv=VCV000209494.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-499G>A|p.?|248/7088|135/5592||499|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-499G>A|p.?|188/7028|-7/5451||499|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-499G>A|p.?|154/3682|135/2280||499|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-499G>A|p.?|242/3696|135/2100||499|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-499G>A|p.?|248/7151|135/5655||499|	GT:AD:DP:GQ	0/1:8,8:16:48
-17	41259079	.	A	ATT	.	.	ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-530_135-529insAA|p.?|248/7088|135/5592||530|,ATT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-530_-7-529insAA|p.?|188/7028|-7/5451||530|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-530_135-529insAA|p.?|154/3682|135/2280||530|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-530_135-529insAA|p.?|242/3696|135/2100||530|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-530_135-529insAA|p.?|248/7151|135/5655||530|	GT:AD:DP:GQ	0/1:10,3:13:7
-17	41259113	.	G	A	.	.	clinvar_vcv=VCV000264811.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-563C>T|p.?|248/7088|135/5592||563|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-563C>T|p.?|188/7028|-7/5451||563|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-563C>T|p.?|154/3682|135/2280||563|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-563C>T|p.?|242/3696|135/2100||563|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-563C>T|p.?|248/7151|135/5655||563|	GT:AD:DP:GQ	0/1:11,8:19:48
-17	41260352	.	C	CA	.	.	clinvar_vcv=VCV000264791.2;clinvar_germline_classification=Benign;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-1803_135-1802insT|p.?|248/7088|135/5592||1803|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-1803_-7-1802insT|p.?|188/7028|-7/5451||1803|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-1803_135-1802insT|p.?|154/3682|135/2280||1803|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-1803_135-1802insT|p.?|242/3696|135/2100||1803|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-1803_135-1802insT|p.?|248/7151|135/5655||1803|	GT:AD:DP:GQ	0/1:11,8:19:43
-17	41260723	.	C	CAAAAA	.	.	ANN=CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2174_135-2173insTTTTT|p.?|248/7088|135/5592||2174|,CAAAAA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2174_-7-2173insTTTTT|p.?|188/7028|-7/5451||2174|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2174_135-2173insTTTTT|p.?|154/3682|135/2280||2174|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2174_135-2173insTTTTT|p.?|242/3696|135/2100||2174|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2174_135-2173insTTTTT|p.?|248/7151|135/5655||2174|	GT:AD:DP:GQ	0/1:1,1:2:20
-17	41260808	.	A	G	.	.	clinvar_vcv=VCV000209499.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2258T>C|p.?|248/7088|135/5592||2258|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2258T>C|p.?|188/7028|-7/5451||2258|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2258T>C|p.?|154/3682|135/2280||2258|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2258T>C|p.?|242/3696|135/2100||2258|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2258T>C|p.?|248/7151|135/5655||2258|	GT:AD:DP:GQ	0/1:12,3:15:32
-17	41261058	.	T	TCTATCTATCTACCTAC	.	.	clinvar_vcv=VCV000264813.2;clinvar_germline_classification=Benign;ANN=TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7088|135/5592||2509|,TCTATCTATCTACCTAC|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2509_-7-2508insGTAGGTAGATAGATAG|p.?|188/7028|-7/5451||2509|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|154/3682|135/2280||2509|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|242/3696|135/2100||2509|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7151|135/5655||2509|	GT:AD:DP:GQ	0/1:9,11:20:48
-17	41261233	.	C	T	.	.	clinvar_vcv=VCV000209503.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2683G>A|p.?|248/7088|135/5592||2683|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2683G>A|p.?|188/7028|-7/5451||2683|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2683G>A|p.?|154/3682|135/2280||2683|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2683G>A|p.?|242/3696|135/2100||2683|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2683G>A|p.?|248/7151|135/5655||2683|	GT:AD:DP:GQ	0/1:12,15:27:48
-17	41263044	.	A	G	.	.	clinvar_vcv=VCV000209512.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-4494T>C|p.?|248/7088|135/5592||4494|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4494T>C|p.?|188/7028|-7/5451||4494|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-4494T>C|p.?|154/3682|135/2280||4494|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4494T>C|p.?|242/3696|135/2100||4494|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4494T>C|p.?|248/7151|135/5655||4494|	GT:AD:DP:GQ	0/1:7,7:14:48
-17	41263117	.	C	CA	.	.	ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-4568_135-4567insT|p.?|248/7088|135/5592||4568|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4568_-7-4567insT|p.?|188/7028|-7/5451||4568|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-4568_135-4567insT|p.?|154/3682|135/2280||4568|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4568_135-4567insT|p.?|242/3696|135/2100||4568|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4568_135-4567insT|p.?|248/7151|135/5655||4568|	GT:AD:DP:GQ	0/1:13,10:23:34
-17	41263566	.	T	C	.	.	clinvar_vcv=VCV000209516.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+4177A>G|p.?|247/7088|134/5592||-4177|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5016A>G|p.?|188/7028|-7/5451||5016|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+4177A>G|p.?|153/3682|134/2280||-4177|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+4177A>G|p.?|241/3696|134/2100||-4177|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+4177A>G|p.?|247/7151|134/5655||-4177|	GT:AD:DP:GQ	0/1:11,8:19:48
-17	41264146	.	G	A	.	.	clinvar_vcv=VCV000209519.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3597C>T|p.?|247/7088|134/5592||-3597|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5596C>T|p.?|188/7028|-7/5451||5596|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3597C>T|p.?|153/3682|134/2280||-3597|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3597C>T|p.?|241/3696|134/2100||-3597|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3597C>T|p.?|247/7151|134/5655||-3597|	GT:AD:DP:GQ	0/1:13,7:20:45
-17	41264364	.	A	G	.	.	clinvar_vcv=VCV000209521.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3379T>C|p.?|247/7088|134/5592||-3379|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5814T>C|p.?|188/7028|-7/5451||5814|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3379T>C|p.?|153/3682|134/2280||-3379|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3379T>C|p.?|241/3696|134/2100||-3379|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3379T>C|p.?|247/7151|134/5655||-3379|	GT:AD:DP:GQ	0/1:8,16:24:45
-17	41264739	.	C	T	.	.	clinvar_vcv=VCV000264785.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3004G>A|p.?|247/7088|134/5592||-3004|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6189G>A|p.?|188/7028|-7/5451||6189|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3004G>A|p.?|153/3682|134/2280||-3004|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3004G>A|p.?|241/3696|134/2100||-3004|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3004G>A|p.?|247/7151|134/5655||-3004|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
-17	41264740	.	TGA	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3001_134+3002delTC|p.?|247/7088|134/5592||-3001|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6192_-7-6191delTC|p.?|188/7028|-7/5451||6191|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3001_134+3002delTC|p.?|153/3682|134/2280||-3001|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3001_134+3002delTC|p.?|241/3696|134/2100||-3001|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3001_134+3002delTC|p.?|247/7151|134/5655||-3001|	GT:AD:DP:GQ	0/1:14,16:30:48
-17	41264743	.	CT	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2999delA|p.?|247/7088|134/5592||-2999|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6194delA|p.?|188/7028|-7/5451||6194|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2999delA|p.?|153/3682|134/2280||-2999|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2999delA|p.?|241/3696|134/2100||-2999|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2999delA|p.?|247/7151|134/5655||-2999|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
-17	41264749	.	C	G	.	.	clinvar_vcv=VCV000264823.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2994G>C|p.?|247/7088|134/5592||-2994|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6199G>C|p.?|188/7028|-7/5451||6199|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2994G>C|p.?|153/3682|134/2280||-2994|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2994G>C|p.?|241/3696|134/2100||-2994|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2994G>C|p.?|247/7151|134/5655||-2994|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
-17	41264750	.	A	T	.	.	clinvar_vcv=VCV000264824.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2993T>A|p.?|247/7088|134/5592||-2993|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6200T>A|p.?|188/7028|-7/5451||6200|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2993T>A|p.?|153/3682|134/2280||-2993|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2993T>A|p.?|241/3696|134/2100||-2993|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2993T>A|p.?|247/7151|134/5655||-2993|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
-17	41264751	.	A	AGGG	.	.	ANN=AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2991_134+2992insCCC|p.?|247/7088|134/5592||-2992|,AGGG|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6202_-7-6201insCCC|p.?|188/7028|-7/5451||6202|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2991_134+2992insCCC|p.?|153/3682|134/2280||-2992|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2991_134+2992insCCC|p.?|241/3696|134/2100||-2992|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2991_134+2992insCCC|p.?|247/7151|134/5655||-2992|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
-17	41264753	.	C	T	.	.	clinvar_vcv=VCV000264819.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2990G>A|p.?|247/7088|134/5592||-2990|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6203G>A|p.?|188/7028|-7/5451||6203|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2990G>A|p.?|153/3682|134/2280||-2990|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2990G>A|p.?|241/3696|134/2100||-2990|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2990G>A|p.?|247/7151|134/5655||-2990|	GT:AD:DP:GQ:PS	0|1:14,13:27:48:41264739
-17	41264755	.	TGAAAC	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2983_134+2987delGTTTC|p.?|247/7088|134/5592||-2983|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6210_-7-6206delGTTTC|p.?|188/7028|-7/5451||6206|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2983_134+2987delGTTTC|p.?|153/3682|134/2280||-2983|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2983_134+2987delGTTTC|p.?|241/3696|134/2100||-2983|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2983_134+2987delGTTTC|p.?|247/7151|134/5655||-2983|	GT:AD:DP:GQ:PS	0|1:14,13:27:48:41264739
-17	41265776	.	A	G	.	.	clinvar_vcv=VCV000209524.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+1967T>C|p.?|247/7088|134/5592||-1967|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7226T>C|p.?|188/7028|-7/5451||7226|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+1967T>C|p.?|153/3682|134/2280||-1967|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1967T>C|p.?|241/3696|134/2100||-1967|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1967T>C|p.?|247/7151|134/5655||-1967|	GT:AD:DP:GQ	0/1:23,14:37:44
-17	41266407	.	C	CT	.	.	clinvar_vcv=VCV000264777.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+1335_134+1336insA|p.?|247/7088|134/5592||-1336|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7858_-7-7857insA|p.?|188/7028|-7/5451||7858|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+1335_134+1336insA|p.?|153/3682|134/2280||-1336|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1335_134+1336insA|p.?|241/3696|134/2100||-1336|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1335_134+1336insA|p.?|247/7151|134/5655||-1336|	GT:AD:DP:GQ	0/1:10,8:18:33
-17	41267050	.	G	A	.	.	clinvar_vcv=VCV000209531.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+693C>T|p.?|247/7088|134/5592||-693|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-8500C>T|p.?|188/7028|-7/5451||8500|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+693C>T|p.?|153/3682|134/2280||-693|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+693C>T|p.?|241/3696|134/2100||-693|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+693C>T|p.?|247/7151|134/5655||-693|	GT:AD:DP:GQ	0/1:7,16:23:44
-17	41267518	.	CA	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+224delT|p.?|247/7088|134/5592||-224|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+8515delT|p.?|187/7028|-8/5451||-8515|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+224delT|p.?|153/3682|134/2280||-224|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+224delT|p.?|241/3696|134/2100||-224|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+224delT|p.?|247/7151|134/5655||-224|	GT:AD:DP:GQ	0/1:11,8:19:35
-17	41268206	.	A	C	.	.	clinvar_vcv=VCV000209537.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-410T>G|p.?|194/7088|81/5592||410|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7828T>G|p.?|187/7028|-8/5451||-7828|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-410T>G|p.?|100/3682|81/2280||410|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-410T>G|p.?|188/3696|81/2100||410|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-410T>G|p.?|194/7151|81/5655||410|	GT:AD:DP:GQ:PS	0|1:13,9:22:46:41268206
-17	41268208	.	C	CT	.	.	clinvar_vcv=VCV000264808.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-413_81-412insA|p.?|194/7088|81/5592||413|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7825_-8+7826insA|p.?|187/7028|-8/5451||-7826|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-413_81-412insA|p.?|100/3682|81/2280||413|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-413_81-412insA|p.?|188/3696|81/2100||413|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-413_81-412insA|p.?|194/7151|81/5655||413|	GT:AD:DP:GQ:PS	0|1:13,9:22:46:41268206
-17	41270229	.	T	G	.	.	clinvar_vcv=VCV000209545.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2433A>C|p.?|194/7088|81/5592||2433|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5805A>C|p.?|187/7028|-8/5451||-5805|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2433A>C|p.?|100/3682|81/2280||2433|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2433A>C|p.?|188/3696|81/2100||2433|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2433A>C|p.?|194/7151|81/5655||2433|	GT:AD:DP:GQ	0/1:7,17:24:40
-17	41270277	.	C	T	.	.	clinvar_vcv=VCV000209547.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2481G>A|p.?|194/7088|81/5592||2481|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5757G>A|p.?|187/7028|-8/5451||-5757|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2481G>A|p.?|100/3682|81/2280||2481|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2481G>A|p.?|188/3696|81/2100||2481|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2481G>A|p.?|194/7151|81/5655||2481|	GT:AD:DP:GQ	0/1:9,13:22:48
-17	41270463	.	G	A	.	.	clinvar_vcv=VCV000209551.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2667C>T|p.?|194/7088|81/5592||2667|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5571C>T|p.?|187/7028|-8/5451||-5571|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2667C>T|p.?|100/3682|81/2280||2667|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2667C>T|p.?|188/3696|81/2100||2667|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2667C>T|p.?|194/7151|81/5655||2667|	GT:AD:DP:GQ	0/1:15,13:28:48
-17	41270666	.	C	A	.	.	clinvar_vcv=VCV000209552.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2870G>T|p.?|194/7088|81/5592||2870|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5368G>T|p.?|187/7028|-8/5451||-5368|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2870G>T|p.?|100/3682|81/2280||2870|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2870G>T|p.?|188/3696|81/2100||2870|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2870G>T|p.?|194/7151|81/5655||2870|	GT:AD:DP:GQ	0/1:11,4:15:43
-17	41270778	.	C	CT	.	.	clinvar_vcv=VCV000264797.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2983_81-2982insA|p.?|194/7088|81/5592||2983|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5255_-8+5256insA|p.?|187/7028|-8/5451||-5256|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2983_81-2982insA|p.?|100/3682|81/2280||2983|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2983_81-2982insA|p.?|188/3696|81/2100||2983|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2983_81-2982insA|p.?|194/7151|81/5655||2983|	GT:AD:DP:GQ	0/1:11,5:16:14
-17	41271293	.	GA	G	.	.	ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-3498delT|p.?|194/7088|81/5592||3498|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+4740delT|p.?|187/7028|-8/5451||-4740|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-3498delT|p.?|100/3682|81/2280||3498|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-3498delT|p.?|188/3696|81/2100||3498|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-3498delT|p.?|194/7151|81/5655||3498|	GT:AD:DP:GQ	0/1:10,10:20:48
-17	41273095	.	G	A	.	.	clinvar_vcv=VCV000209559.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2939C>T|p.?|193/7088|80/5592||-2939|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2939C>T|p.?|187/7028|-8/5451||-2939|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2939C>T|p.?|99/3682|80/2280||-2939|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2939C>T|p.?|187/3696|80/2100||-2939|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2939C>T|p.?|193/7151|80/5655||-2939|	GT:AD:DP:GQ	0/1:12,8:20:47
-17	41273348	.	T	C	.	.	clinvar_vcv=VCV000209561.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2686A>G|p.?|193/7088|80/5592||-2686|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2686A>G|p.?|187/7028|-8/5451||-2686|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2686A>G|p.?|99/3682|80/2280||-2686|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2686A>G|p.?|187/3696|80/2100||-2686|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2686A>G|p.?|193/7151|80/5655||-2686|	GT:AD:DP:GQ	0/1:18,13:31:47
-17	41273379	.	G	C	.	.	clinvar_vcv=VCV000209562.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2655C>G|p.?|193/7088|80/5592||-2655|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2655C>G|p.?|187/7028|-8/5451||-2655|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2655C>G|p.?|99/3682|80/2280||-2655|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2655C>G|p.?|187/3696|80/2100||-2655|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2655C>G|p.?|193/7151|80/5655||-2655|	GT:AD:DP:GQ	0/1:19,14:33:47
-17	41273537	.	A	C	.	.	clinvar_vcv=VCV000209564.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2497T>G|p.?|193/7088|80/5592||-2497|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2497T>G|p.?|187/7028|-8/5451||-2497|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2497T>G|p.?|99/3682|80/2280||-2497|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2497T>G|p.?|187/3696|80/2100||-2497|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2497T>G|p.?|193/7151|80/5655||-2497|	GT:AD:DP:GQ	0/1:14,19:33:48
-17	41274778	.	G	A	.	.	clinvar_vcv=VCV000209565.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+1256C>T|p.?|193/7088|80/5592||-1256|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1256C>T|p.?|187/7028|-8/5451||-1256|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+1256C>T|p.?|99/3682|80/2280||-1256|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1256C>T|p.?|187/3696|80/2100||-1256|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1256C>T|p.?|193/7151|80/5655||-1256|	GT:AD:DP:GQ	0/1:11,16:27:48
-17	41274906	.	G	A	.	.	clinvar_vcv=VCV000209568.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+1128C>T|p.?|193/7088|80/5592||-1128|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1128C>T|p.?|187/7028|-8/5451||-1128|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+1128C>T|p.?|99/3682|80/2280||-1128|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1128C>T|p.?|187/3696|80/2100||-1128|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1128C>T|p.?|193/7151|80/5655||-1128|	GT:AD:DP:GQ	0/1:17,10:27:47
-17	41275081	.	G	GA	.	.	clinvar_vcv=VCV000209569.2;clinvar_germline_classification=Benign;ANN=GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+952_80+953insT|p.?|193/7088|80/5592||-953|,GA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+952_-8+953insT|p.?|187/7028|-8/5451||-953|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+952_80+953insT|p.?|99/3682|80/2280||-953|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+952_80+953insT|p.?|187/3696|80/2100||-953|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+952_80+953insT|p.?|193/7151|80/5655||-953|	GT:AD:DP:GQ	0/1:10,12:22:47
-17	41275151	.	G	C	.	.	clinvar_vcv=VCV000209570.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+883C>G|p.?|193/7088|80/5592||-883|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+883C>G|p.?|187/7028|-8/5451||-883|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+883C>G|p.?|99/3682|80/2280||-883|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+883C>G|p.?|187/3696|80/2100||-883|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+883C>G|p.?|193/7151|80/5655||-883|	GT:AD:DP:GQ	0/1:15,13:28:48
-17	41275366	.	GTTTTTTT	G	.	.	ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+661_80+667delAAAAAAA|p.?|193/7088|80/5592||-661|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+661_-8+667delAAAAAAA|p.?|187/7028|-8/5451||-661|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+661_80+667delAAAAAAA|p.?|99/3682|80/2280||-661|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+661_80+667delAAAAAAA|p.?|187/3696|80/2100||-661|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+661_80+667delAAAAAAA|p.?|193/7151|80/5655||-661|	GT:AD:DP:GQ	0/1:10,11:21:48
-17	41275645	.	A	G	.	.	clinvar_vcv=VCV000209571.3;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+389T>C|p.?|193/7088|80/5592||-389|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+389T>C|p.?|187/7028|-8/5451||-389|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+389T>C|p.?|99/3682|80/2280||-389|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+389T>C|p.?|187/3696|80/2100||-389|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+389T>C|p.?|193/7151|80/5655||-389|	GT:AD:DP:GQ	0/1:15,17:32:48
-17	41276247	.	A	G	.	.	gnomad_exomes_an=31318;gnomad_exomes_hom=1611;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125468.4;clinvar_germline_classification=Benign;ANN=G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-19-115T>C|p.?|95/7088|-19/5592||115|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-115T>C|p.?|89/7028|-106/5451||115|,G|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||115|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-115T>C|p.?|89/3696|-19/2100||115|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-115T>C|p.?|95/7151|-19/5655||115|	GT:AD:DP:GQ	0/1:18,10:28:44
-17	41276348	.	T	C	.	.	clinvar_vcv=VCV000209574.3;clinvar_germline_classification=Benign;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-19-216A>G|p.?|95/7088|-19/5592||216|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-216A>G|p.?|89/7028|-106/5451||216|,C|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||216|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-216A>G|p.?|89/3696|-19/2100||216|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-216A>G|p.?|95/7151|-19/5655||216|	GT:AD:DP:GQ	0/1:17,13:30:47
-17	41277187	.	G	C	.	.	gnomad_exomes_an=29432;gnomad_exomes_hom=4088;gnomad_exomes_het=6345;gnomad_genomes_an=128296;gnomad_genomes_hom=11705;gnomad_genomes_het=29182;clinvar_vcv=VCV000189123.4;clinvar_germline_classification=Benign;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-20+101C>G|p.?|94/7088|-20/5592||-101|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-107+107C>G|p.?|88/7028|-107/5451||-107|,C|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||1055|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-20+107C>G|p.?|88/3696|-20/2100||-107|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-20+101C>G|p.?|94/7151|-20/5655||-101|	GT:AD:DP:GQ	0/1:14,14:28:48
+17	41244000	.	T	C	.	.	gnomad_exomes_an=31346;gnomad_exomes_hom=1591;gnomad_exomes_het=6707;gnomad_genomes_an=250954;gnomad_genomes_hom=16402;gnomad_genomes_het=55703;clinvar_vcv=VCV000041818.87;clinvar_germline_classification=Benign;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.3548A>G|p.Lys1183Arg|3661/7088|3548/5592|1183/1864|0|-1|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.3407A>G|p.Lys1136Arg|3601/7028|3407/5451|1136/1817|0|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.788-951A>G|p.?|807/3682|788/2280||951|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-951A>G|p.?|895/3696|788/2100||951|-1|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3548A>G|p.Lys1183Arg|3661/7151|3548/5655|1183/1885|0|-1|	GT:AD:DP:GQ	0/1:8,18:26:43
+17	41244435	.	T	C	.	.	gnomad_exomes_an=31332;gnomad_exomes_hom=1505;gnomad_exomes_het=6415;gnomad_genomes_an=251032;gnomad_genomes_hom=16145;gnomad_genomes_het=55137;clinvar_vcv=VCV000041815.87;clinvar_germline_classification=Benign;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.3113A>G|p.Glu1038Gly|3226/7088|3113/5592|1038/1864|0|-1|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2972A>G|p.Glu991Gly|3166/7028|2972/5451|991/1817|0|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.788-1386A>G|p.?|807/3682|788/2280||1386|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-1386A>G|p.?|895/3696|788/2100||1386|-1|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3113A>G|p.Glu1038Gly|3226/7151|3113/5655|1038/1885|0|-1|	GT:AD:DP:GQ	0/1:12,14:26:47
+17	41244936	.	G	A	.	.	gnomad_exomes_an=31324;gnomad_exomes_hom=4287;gnomad_exomes_het=6594;gnomad_genomes_an=251034;gnomad_genomes_hom=22738;gnomad_genomes_het=55898;clinvar_vcv=VCV000041812.88;clinvar_germline_classification=Benign;ANN=A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2612C>T|p.Pro871Leu|2725/7088|2612/5592|871/1864|0|-1|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2471C>T|p.Pro824Leu|2665/7028|2471/5451|824/1817|0|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1825C>T|p.?|806/3682|787/2280||-1825|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1825C>T|p.?|894/3696|787/2100||-1825|-1|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2612C>T|p.Pro871Leu|2725/7151|2612/5655|871/1885|0|-1|	GT:AD:DP:GQ	0/1:17,13:30:47
+17	41245237	.	A	G	.	.	gnomad_exomes_an=31314;gnomad_exomes_hom=1492;gnomad_exomes_het=6416;gnomad_genomes_an=250946;gnomad_genomes_hom=16057;gnomad_genomes_het=55063;clinvar_vcv=VCV000125554.83;clinvar_germline_classification=Benign;ANN=G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2311T>C|p.Leu771=|2424/7088|2311/5592|771/1864|0|-1|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2170T>C|p.Leu724=|2364/7028|2170/5451|724/1817|0|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1524T>C|p.?|806/3682|787/2280||-1524|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1524T>C|p.?|894/3696|787/2100||-1524|-1|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2311T>C|p.Leu771=|2424/7151|2311/5655|771/1885|0|-1|	GT:AD:DP:GQ	0/1:18,11:29:46
+17	41245466	.	G	A	.	.	gnomad_exomes_an=31338;gnomad_exomes_hom=1602;gnomad_exomes_het=6709;gnomad_genomes_an=251110;gnomad_genomes_hom=16420;gnomad_genomes_het=55707;clinvar_vcv=VCV000125536.84;clinvar_germline_classification=Benign;ANN=A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2082C>T|p.Ser694=|2195/7088|2082/5592|694/1864|0|-1|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.1941C>T|p.Ser647=|2135/7028|1941/5451|647/1817|0|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1295C>T|p.?|806/3682|787/2280||-1295|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1295C>T|p.?|894/3696|787/2100||-1295|-1|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2082C>T|p.Ser694=|2195/7151|2082/5655|694/1885|0|-1|	GT:AD:DP:GQ	0/1:11,8:19:48
+17	41247122	.	A	ACCT	.	.	clinvar_vcv=VCV000127125.5;clinvar_germline_classification=Benign;ANN=ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|9/22|c.671-246_671-245insAGG|p.?|784/7088|671/5592||246|-1|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.530-246_530-245insAGG|p.?|724/7028|530/5451||246|-1|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|8/21|c.671-246_671-245insAGG|p.?|690/3682|671/2280||246|-1|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.671-246_671-245insAGG|p.?|778/3696|671/2100||246|-1|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.671-246_671-245insAGG|p.?|784/7151|671/5655||246|-1|	GT:AD:DP:GQ	0/1:18,11:29:45
+17	41247604	.	A	C	.	.	clinvar_vcv=VCV000209447.5;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|9/22|c.670+259T>G|p.?|783/7088|670/5592||-259|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.529+259T>G|p.?|723/7028|529/5451||-259|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|8/21|c.670+259T>G|p.?|689/3682|670/2280||-259|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.670+259T>G|p.?|777/3696|670/2100||-259|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.670+259T>G|p.?|783/7151|670/5655||-259|-1|	GT:AD:DP:GQ	0/1:12,11:23:47
+17	41248164	.	C	T	.	.	clinvar_vcv=VCV000209449.4;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-225G>A|p.?|707/7088|594/5592||225|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-225G>A|p.?|647/7028|453/5451||225|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-225G>A|p.?|613/3682|594/2280||225|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-225G>A|p.?|701/3696|594/2100||225|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-225G>A|p.?|707/7151|594/5655||225|-1|	GT:AD:DP:GQ	0/1:14,7:21:44
+17	41248393	.	C	CAAAAAAAAAA	.	.	ANN=CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-455_594-454insTTTTTTTTTT|p.?|707/7088|594/5592||455|-1|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-455_453-454insTTTTTTTTTT|p.?|647/7028|453/5451||455|-1|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-455_594-454insTTTTTTTTTT|p.?|613/3682|594/2280||455|-1|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-455_594-454insTTTTTTTTTT|p.?|701/3696|594/2100||455|-1|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-455_594-454insTTTTTTTTTT|p.?|707/7151|594/5655||455|-1|	GT:AD:DP:GQ	0/1:9,7:16:48
+17	41248484	.	G	C	.	.	clinvar_vcv=VCV000209450.4;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-545C>G|p.?|707/7088|594/5592||545|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-545C>G|p.?|647/7028|453/5451||545|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-545C>G|p.?|613/3682|594/2280||545|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-545C>G|p.?|701/3696|594/2100||545|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-545C>G|p.?|707/7151|594/5655||545|-1|	GT:AD:DP:GQ	0/1:11,9:20:48
+17	41248588	.	CA	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-650del|p.?|707/7088|594/5592||650|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-650del|p.?|647/7028|453/5451||650|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-650del|p.?|613/3682|594/2280||650|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-650del|p.?|701/3696|594/2100||650|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-650del|p.?|707/7151|594/5655||650|-1|	GT:AD:DP:GQ	0/1:9,10:19:42
+17	41249094	.	A	G	.	.	gnomad_exomes_an=31332;gnomad_exomes_hom=1602;gnomad_exomes_het=6703;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000209451.5;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.593+167T>C|p.?|706/7088|593/5592||-167|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.452+167T>C|p.?|646/7028|452/5451||-167|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.593+167T>C|p.?|612/3682|593/2280||-167|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.593+167T>C|p.?|700/3696|593/2100||-167|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.593+167T>C|p.?|706/7151|593/5655||-167|-1|	GT:AD:DP:GQ	0/1:9,7:16:48
+17	41249363	.	TA	T	.	.	gnomad_exomes_an=31286;gnomad_exomes_hom=1497;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.548-58del|p.?|661/7088|548/5592||58|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-58del|p.?|601/7028|407/5451||58|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.548-58del|p.?|567/3682|548/2280||58|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-58del|p.?|655/3696|548/2100||58|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-58del|p.?|661/7151|548/5655||58|-1|	GT:AD:DP:GQ	0/1:12,13:25:48
+17	41250047	.	C	CT	.	.	ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.548-742_548-741insA|p.?|661/7088|548/5592||742|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-742_407-741insA|p.?|601/7028|407/5451||742|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.548-742_548-741insA|p.?|567/3682|548/2280||742|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-742_548-741insA|p.?|655/3696|548/2100||742|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-742_548-741insA|p.?|661/7151|548/5655||742|-1|	GT:AD:DP:GQ	0/1:13,7:20:18
+17	41250678	.	C	CT	.	.	clinvar_vcv=VCV000209458.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+1113_547+1114insA|p.?|660/7088|547/5592||-1114|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+1113_406+1114insA|p.?|600/7028|406/5451||-1114|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+1113_547+1114insA|p.?|566/3682|547/2280||-1114|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+1113_547+1114insA|p.?|654/3696|547/2100||-1114|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+1113_547+1114insA|p.?|660/7151|547/5655||-1114|-1|	GT:AD:DP:GQ	0/1:6,16:22:42
+17	41250923	.	T	C	.	.	clinvar_vcv=VCV000209460.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+869A>G|p.?|660/7088|547/5592||-869|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+869A>G|p.?|600/7028|406/5451||-869|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+869A>G|p.?|566/3682|547/2280||-869|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+869A>G|p.?|654/3696|547/2100||-869|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+869A>G|p.?|660/7151|547/5655||-869|-1|	GT:AD:DP:GQ	0/1:13,9:22:47
+17	41251495	.	C	G	.	.	clinvar_vcv=VCV000209463.4;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+297G>C|p.?|660/7088|547/5592||-297|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+297G>C|p.?|600/7028|406/5451||-297|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+297G>C|p.?|566/3682|547/2280||-297|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+297G>C|p.?|654/3696|547/2100||-297|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+297G>C|p.?|660/7151|547/5655||-297|-1|	GT:AD:DP:GQ	0/1:11,15:26:48
+17	41251646	.	T	A	.	.	gnomad_exomes_an=31294;gnomad_exomes_hom=1592;gnomad_exomes_het=6693;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125879.7;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+146A>T|p.?|660/7088|547/5592||-146|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+146A>T|p.?|600/7028|406/5451||-146|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+146A>T|p.?|566/3682|547/2280||-146|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+146A>T|p.?|654/3696|547/2100||-146|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+146A>T|p.?|660/7151|547/5655||-146|-1|	GT:AD:DP:GQ	0/1:11,8:19:48
+17	41252575	.	G	A	.	.	clinvar_vcv=VCV000209466.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-678C>T|p.?|555/7088|442/5592||678|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-678C>T|p.?|495/7028|301/5451||678|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-678C>T|p.?|461/3682|442/2280||678|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-678C>T|p.?|549/3696|442/2100||678|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-678C>T|p.?|555/7151|442/5655||678|-1|	GT:AD:DP:GQ:PS	1|1:0,3:3:5:41252575
+17	41252591	.	C	CAT	.	.	clinvar_vcv=VCV000264796.2;clinvar_germline_classification=Benign;ANN=CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-695_442-694insAT|p.?|555/7088|442/5592||695|-1|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-695_301-694insAT|p.?|495/7028|301/5451||695|-1|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-695_442-694insAT|p.?|461/3682|442/2280||695|-1|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-695_442-694insAT|p.?|549/3696|442/2100||695|-1|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-695_442-694insAT|p.?|555/7151|442/5655||695|-1|	GT:AD:DP:GQ:PS	1|1:0,2:2:4:41252575
+17	41254174	.	A	G	.	.	clinvar_vcv=VCV000209478.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1965T>C|p.?|554/7088|441/5592||-1965|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1965T>C|p.?|494/7028|300/5451||-1965|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1965T>C|p.?|460/3682|441/2280||-1965|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1965T>C|p.?|548/3696|441/2100||-1965|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1965T>C|p.?|554/7151|441/5655||-1965|-1|	GT:AD:DP:GQ	0/1:14,13:27:48
+17	41254374	.	C	CTTTTTTTT	.	.	ANN=CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1764_441+1765insAAAAAAAA|p.?|554/7088|441/5592||-1765|-1|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1764_300+1765insAAAAAAAA|p.?|494/7028|300/5451||-1765|-1|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1764_441+1765insAAAAAAAA|p.?|460/3682|441/2280||-1765|-1|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1764_441+1765insAAAAAAAA|p.?|548/3696|441/2100||-1765|-1|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1764_441+1765insAAAAAAAA|p.?|554/7151|441/5655||-1765|-1|	GT:AD:DP:GQ	0/1:6,7:13:48
+17	41254405	.	C	T	.	.	clinvar_vcv=VCV000264778.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1734G>A|p.?|554/7088|441/5592||-1734|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1734G>A|p.?|494/7028|300/5451||-1734|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1734G>A|p.?|460/3682|441/2280||-1734|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1734G>A|p.?|548/3696|441/2100||-1734|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1734G>A|p.?|554/7151|441/5655||-1734|-1|	GT:AD:DP:GQ	0/1:5,9:14:43
+17	41254486	.	T	G	.	.	clinvar_vcv=VCV000209479.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1653A>C|p.?|554/7088|441/5592||-1653|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1653A>C|p.?|494/7028|300/5451||-1653|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1653A>C|p.?|460/3682|441/2280||-1653|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1653A>C|p.?|548/3696|441/2100||-1653|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1653A>C|p.?|554/7151|441/5655||-1653|-1|	GT:AD:DP:GQ	0/1:8,15:23:46
+17	41254965	.	C	CT	.	.	clinvar_vcv=VCV000264845.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1173_441+1174insA|p.?|554/7088|441/5592||-1174|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1173_300+1174insA|p.?|494/7028|300/5451||-1174|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1173_441+1174insA|p.?|460/3682|441/2280||-1174|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1173_441+1174insA|p.?|548/3696|441/2100||-1174|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1173_441+1174insA|p.?|554/7151|441/5655||-1174|-1|	GT:AD:DP:GQ	0/1:14,8:22:22
+17	41255102	.	A	G	.	.	clinvar_vcv=VCV000209483.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1037T>C|p.?|554/7088|441/5592||-1037|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1037T>C|p.?|494/7028|300/5451||-1037|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1037T>C|p.?|460/3682|441/2280||-1037|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1037T>C|p.?|548/3696|441/2100||-1037|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1037T>C|p.?|554/7151|441/5655||-1037|-1|	GT:AD:DP:GQ:PS	0|1:19,12:31:46:41255102
+17	41255111	.	A	T	.	.	clinvar_vcv=VCV000209484.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1028T>A|p.?|554/7088|441/5592||-1028|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1028T>A|p.?|494/7028|300/5451||-1028|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1028T>A|p.?|460/3682|441/2280||-1028|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1028T>A|p.?|548/3696|441/2100||-1028|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1028T>A|p.?|554/7151|441/5655||-1028|-1|	GT:AD:DP:GQ:PS	0|1:19,12:31:46:41255102
+17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64del|p.?|554/7088|441/5592||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64del|p.?|494/7028|300/5451||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64del|p.?|460/3682|441/2280||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64del|p.?|548/3696|441/2100||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64del|p.?|554/7151|441/5655||-64|-1|	GT:AD:DP:GQ:PS	0|1:11,6:17:43:41256074
+17	41256089	.	AAAAAAAAAGAAAAG	A	.	.	gnomad_exomes_an=28388;gnomad_exomes_hom=1079;gnomad_exomes_het=5744;gnomad_genomes_an=167932;gnomad_genomes_hom=9911;gnomad_genomes_het=23697;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+36_441+49del|p.?|554/7088|441/5592||-36|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+36_300+49del|p.?|494/7028|300/5451||-36|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+36_441+49del|p.?|460/3682|441/2280||-36|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+36_441+49del|p.?|548/3696|441/2100||-36|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+36_441+49del|p.?|554/7151|441/5655||-36|-1|	GT:AD:DP:GQ:PS	0|1:13,6:19:43:41256074
+17	41257134	.	T	C	.	.	gnomad_exomes_an=31346;gnomad_exomes_hom=4418;gnomad_exomes_het=6505;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125614.7;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.213-161A>G|p.?|326/7088|213/5592||161|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-161A>G|p.?|266/7028|72/5451||161|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.213-161A>G|p.?|232/3682|213/2280||161|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-161A>G|p.?|320/3696|213/2100||161|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-161A>G|p.?|326/7151|213/5655||161|-1|	GT:AD:DP:GQ	0/1:14,15:29:48
+17	41257458	.	A	C	.	.	clinvar_vcv=VCV000209489.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.213-485T>G|p.?|326/7088|213/5592||485|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-485T>G|p.?|266/7028|72/5451||485|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.213-485T>G|p.?|232/3682|213/2280||485|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-485T>G|p.?|320/3696|213/2100||485|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-485T>G|p.?|326/7151|213/5655||485|-1|	GT:AD:DP:GQ	0/1:11,15:26:48
+17	41258043	.	C	T	.	.	clinvar_vcv=VCV000209491.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.212+430G>A|p.?|325/7088|212/5592||-430|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+430G>A|p.?|265/7028|71/5451||-430|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.212+430G>A|p.?|231/3682|212/2280||-430|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+430G>A|p.?|319/3696|212/2100||-430|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+430G>A|p.?|325/7151|212/5655||-430|-1|	GT:AD:DP:GQ	0/1:14,13:27:48
+17	41258135	.	T	TA	.	.	ANN=TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.212+337_212+338insT|p.?|325/7088|212/5592||-338|-1|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+337_71+338insT|p.?|265/7028|71/5451||-338|-1|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.212+337_212+338insT|p.?|231/3682|212/2280||-338|-1|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+337_212+338insT|p.?|319/3696|212/2100||-338|-1|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+337_212+338insT|p.?|325/7151|212/5655||-338|-1|	GT:AD:DP:GQ	1/1:3,11:14:4
+17	41259049	.	C	T	.	.	clinvar_vcv=VCV000209494.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-499G>A|p.?|248/7088|135/5592||499|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-499G>A|p.?|188/7028|-7/5451||499|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-499G>A|p.?|154/3682|135/2280||499|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-499G>A|p.?|242/3696|135/2100||499|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-499G>A|p.?|248/7151|135/5655||499|-1|	GT:AD:DP:GQ	0/1:8,8:16:48
+17	41259079	.	A	ATT	.	.	ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-530_135-529insAA|p.?|248/7088|135/5592||530|-1|,ATT|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-530_-7-529insAA|p.?|188/7028|-7/5451||530|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-530_135-529insAA|p.?|154/3682|135/2280||530|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-530_135-529insAA|p.?|242/3696|135/2100||530|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-530_135-529insAA|p.?|248/7151|135/5655||530|-1|	GT:AD:DP:GQ	0/1:10,3:13:7
+17	41259113	.	G	A	.	.	clinvar_vcv=VCV000264811.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-563C>T|p.?|248/7088|135/5592||563|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-563C>T|p.?|188/7028|-7/5451||563|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-563C>T|p.?|154/3682|135/2280||563|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-563C>T|p.?|242/3696|135/2100||563|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-563C>T|p.?|248/7151|135/5655||563|-1|	GT:AD:DP:GQ	0/1:11,8:19:48
+17	41260352	.	C	CA	.	.	clinvar_vcv=VCV000264791.2;clinvar_germline_classification=Benign;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-1803_135-1802insT|p.?|248/7088|135/5592||1803|-1|,CA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-1803_-7-1802insT|p.?|188/7028|-7/5451||1803|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-1803_135-1802insT|p.?|154/3682|135/2280||1803|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-1803_135-1802insT|p.?|242/3696|135/2100||1803|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-1803_135-1802insT|p.?|248/7151|135/5655||1803|-1|	GT:AD:DP:GQ	0/1:11,8:19:43
+17	41260723	.	C	CAAAAA	.	.	ANN=CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2174_135-2173insTTTTT|p.?|248/7088|135/5592||2174|-1|,CAAAAA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2174_-7-2173insTTTTT|p.?|188/7028|-7/5451||2174|-1|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2174_135-2173insTTTTT|p.?|154/3682|135/2280||2174|-1|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2174_135-2173insTTTTT|p.?|242/3696|135/2100||2174|-1|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2174_135-2173insTTTTT|p.?|248/7151|135/5655||2174|-1|	GT:AD:DP:GQ	0/1:1,1:2:20
+17	41260808	.	A	G	.	.	clinvar_vcv=VCV000209499.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2258T>C|p.?|248/7088|135/5592||2258|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2258T>C|p.?|188/7028|-7/5451||2258|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2258T>C|p.?|154/3682|135/2280||2258|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2258T>C|p.?|242/3696|135/2100||2258|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2258T>C|p.?|248/7151|135/5655||2258|-1|	GT:AD:DP:GQ	0/1:12,3:15:32
+17	41261058	.	T	TCTATCTATCTACCTAC	.	.	clinvar_vcv=VCV000264813.2;clinvar_germline_classification=Benign;ANN=TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7088|135/5592||2509|-1|,TCTATCTATCTACCTAC|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2509_-7-2508insGTAGGTAGATAGATAG|p.?|188/7028|-7/5451||2509|-1|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|154/3682|135/2280||2509|-1|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|242/3696|135/2100||2509|-1|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7151|135/5655||2509|-1|	GT:AD:DP:GQ	0/1:9,11:20:48
+17	41261233	.	C	T	.	.	clinvar_vcv=VCV000209503.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2683G>A|p.?|248/7088|135/5592||2683|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2683G>A|p.?|188/7028|-7/5451||2683|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2683G>A|p.?|154/3682|135/2280||2683|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2683G>A|p.?|242/3696|135/2100||2683|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2683G>A|p.?|248/7151|135/5655||2683|-1|	GT:AD:DP:GQ	0/1:12,15:27:48
+17	41263044	.	A	G	.	.	clinvar_vcv=VCV000209512.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-4494T>C|p.?|248/7088|135/5592||4494|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4494T>C|p.?|188/7028|-7/5451||4494|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-4494T>C|p.?|154/3682|135/2280||4494|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4494T>C|p.?|242/3696|135/2100||4494|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4494T>C|p.?|248/7151|135/5655||4494|-1|	GT:AD:DP:GQ	0/1:7,7:14:48
+17	41263117	.	C	CA	.	.	ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-4568_135-4567insT|p.?|248/7088|135/5592||4568|-1|,CA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4568_-7-4567insT|p.?|188/7028|-7/5451||4568|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-4568_135-4567insT|p.?|154/3682|135/2280||4568|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4568_135-4567insT|p.?|242/3696|135/2100||4568|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4568_135-4567insT|p.?|248/7151|135/5655||4568|-1|	GT:AD:DP:GQ	0/1:13,10:23:34
+17	41263566	.	T	C	.	.	clinvar_vcv=VCV000209516.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+4177A>G|p.?|247/7088|134/5592||-4177|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5016A>G|p.?|188/7028|-7/5451||5016|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+4177A>G|p.?|153/3682|134/2280||-4177|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+4177A>G|p.?|241/3696|134/2100||-4177|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+4177A>G|p.?|247/7151|134/5655||-4177|-1|	GT:AD:DP:GQ	0/1:11,8:19:48
+17	41264146	.	G	A	.	.	clinvar_vcv=VCV000209519.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3597C>T|p.?|247/7088|134/5592||-3597|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5596C>T|p.?|188/7028|-7/5451||5596|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3597C>T|p.?|153/3682|134/2280||-3597|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3597C>T|p.?|241/3696|134/2100||-3597|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3597C>T|p.?|247/7151|134/5655||-3597|-1|	GT:AD:DP:GQ	0/1:13,7:20:45
+17	41264364	.	A	G	.	.	clinvar_vcv=VCV000209521.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3379T>C|p.?|247/7088|134/5592||-3379|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5814T>C|p.?|188/7028|-7/5451||5814|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3379T>C|p.?|153/3682|134/2280||-3379|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3379T>C|p.?|241/3696|134/2100||-3379|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3379T>C|p.?|247/7151|134/5655||-3379|-1|	GT:AD:DP:GQ	0/1:8,16:24:45
+17	41264739	.	C	T	.	.	clinvar_vcv=VCV000264785.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3004G>A|p.?|247/7088|134/5592||-3004|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6189G>A|p.?|188/7028|-7/5451||6189|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3004G>A|p.?|153/3682|134/2280||-3004|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3004G>A|p.?|241/3696|134/2100||-3004|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3004G>A|p.?|247/7151|134/5655||-3004|-1|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
+17	41264740	.	TGA	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3001_134+3002del|p.?|247/7088|134/5592||-3001|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6192_-7-6191del|p.?|188/7028|-7/5451||6191|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3001_134+3002del|p.?|153/3682|134/2280||-3001|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3001_134+3002del|p.?|241/3696|134/2100||-3001|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3001_134+3002del|p.?|247/7151|134/5655||-3001|-1|	GT:AD:DP:GQ	0/1:14,16:30:48
+17	41264743	.	CT	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2999del|p.?|247/7088|134/5592||-2999|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6194del|p.?|188/7028|-7/5451||6194|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2999del|p.?|153/3682|134/2280||-2999|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2999del|p.?|241/3696|134/2100||-2999|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2999del|p.?|247/7151|134/5655||-2999|-1|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
+17	41264749	.	C	G	.	.	clinvar_vcv=VCV000264823.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2994G>C|p.?|247/7088|134/5592||-2994|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6199G>C|p.?|188/7028|-7/5451||6199|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2994G>C|p.?|153/3682|134/2280||-2994|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2994G>C|p.?|241/3696|134/2100||-2994|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2994G>C|p.?|247/7151|134/5655||-2994|-1|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
+17	41264750	.	A	T	.	.	clinvar_vcv=VCV000264824.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2993T>A|p.?|247/7088|134/5592||-2993|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6200T>A|p.?|188/7028|-7/5451||6200|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2993T>A|p.?|153/3682|134/2280||-2993|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2993T>A|p.?|241/3696|134/2100||-2993|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2993T>A|p.?|247/7151|134/5655||-2993|-1|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
+17	41264751	.	A	AGGG	.	.	ANN=AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2991_134+2992insCCC|p.?|247/7088|134/5592||-2992|-1|,AGGG|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6202_-7-6201insCCC|p.?|188/7028|-7/5451||6202|-1|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2991_134+2992insCCC|p.?|153/3682|134/2280||-2992|-1|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2991_134+2992insCCC|p.?|241/3696|134/2100||-2992|-1|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2991_134+2992insCCC|p.?|247/7151|134/5655||-2992|-1|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
+17	41264753	.	C	T	.	.	clinvar_vcv=VCV000264819.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2990G>A|p.?|247/7088|134/5592||-2990|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6203G>A|p.?|188/7028|-7/5451||6203|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2990G>A|p.?|153/3682|134/2280||-2990|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2990G>A|p.?|241/3696|134/2100||-2990|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2990G>A|p.?|247/7151|134/5655||-2990|-1|	GT:AD:DP:GQ:PS	0|1:14,13:27:48:41264739
+17	41264755	.	TGAAAC	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2983_134+2987del|p.?|247/7088|134/5592||-2983|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6210_-7-6206del|p.?|188/7028|-7/5451||6206|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2983_134+2987del|p.?|153/3682|134/2280||-2983|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2983_134+2987del|p.?|241/3696|134/2100||-2983|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2983_134+2987del|p.?|247/7151|134/5655||-2983|-1|	GT:AD:DP:GQ:PS	0|1:14,13:27:48:41264739
+17	41265776	.	A	G	.	.	clinvar_vcv=VCV000209524.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+1967T>C|p.?|247/7088|134/5592||-1967|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7226T>C|p.?|188/7028|-7/5451||7226|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+1967T>C|p.?|153/3682|134/2280||-1967|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1967T>C|p.?|241/3696|134/2100||-1967|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1967T>C|p.?|247/7151|134/5655||-1967|-1|	GT:AD:DP:GQ	0/1:23,14:37:44
+17	41266407	.	C	CT	.	.	clinvar_vcv=VCV000264777.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+1335_134+1336insA|p.?|247/7088|134/5592||-1336|-1|,CT|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7858_-7-7857insA|p.?|188/7028|-7/5451||7858|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+1335_134+1336insA|p.?|153/3682|134/2280||-1336|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1335_134+1336insA|p.?|241/3696|134/2100||-1336|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1335_134+1336insA|p.?|247/7151|134/5655||-1336|-1|	GT:AD:DP:GQ	0/1:10,8:18:33
+17	41267050	.	G	A	.	.	clinvar_vcv=VCV000209531.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+693C>T|p.?|247/7088|134/5592||-693|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-8500C>T|p.?|188/7028|-7/5451||8500|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+693C>T|p.?|153/3682|134/2280||-693|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+693C>T|p.?|241/3696|134/2100||-693|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+693C>T|p.?|247/7151|134/5655||-693|-1|	GT:AD:DP:GQ	0/1:7,16:23:44
+17	41267518	.	CA	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+224del|p.?|247/7088|134/5592||-224|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+8515del|p.?|187/7028|-8/5451||-8515|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+224del|p.?|153/3682|134/2280||-224|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+224del|p.?|241/3696|134/2100||-224|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+224del|p.?|247/7151|134/5655||-224|-1|	GT:AD:DP:GQ	0/1:11,8:19:35
+17	41268206	.	A	C	.	.	clinvar_vcv=VCV000209537.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-410T>G|p.?|194/7088|81/5592||410|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7828T>G|p.?|187/7028|-8/5451||-7828|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-410T>G|p.?|100/3682|81/2280||410|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-410T>G|p.?|188/3696|81/2100||410|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-410T>G|p.?|194/7151|81/5655||410|-1|	GT:AD:DP:GQ:PS	0|1:13,9:22:46:41268206
+17	41268208	.	C	CT	.	.	clinvar_vcv=VCV000264808.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-413_81-412insA|p.?|194/7088|81/5592||413|-1|,CT|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7825_-8+7826insA|p.?|187/7028|-8/5451||-7826|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-413_81-412insA|p.?|100/3682|81/2280||413|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-413_81-412insA|p.?|188/3696|81/2100||413|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-413_81-412insA|p.?|194/7151|81/5655||413|-1|	GT:AD:DP:GQ:PS	0|1:13,9:22:46:41268206
+17	41270229	.	T	G	.	.	clinvar_vcv=VCV000209545.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2433A>C|p.?|194/7088|81/5592||2433|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5805A>C|p.?|187/7028|-8/5451||-5805|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2433A>C|p.?|100/3682|81/2280||2433|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2433A>C|p.?|188/3696|81/2100||2433|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2433A>C|p.?|194/7151|81/5655||2433|-1|	GT:AD:DP:GQ	0/1:7,17:24:40
+17	41270277	.	C	T	.	.	clinvar_vcv=VCV000209547.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2481G>A|p.?|194/7088|81/5592||2481|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5757G>A|p.?|187/7028|-8/5451||-5757|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2481G>A|p.?|100/3682|81/2280||2481|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2481G>A|p.?|188/3696|81/2100||2481|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2481G>A|p.?|194/7151|81/5655||2481|-1|	GT:AD:DP:GQ	0/1:9,13:22:48
+17	41270463	.	G	A	.	.	clinvar_vcv=VCV000209551.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2667C>T|p.?|194/7088|81/5592||2667|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5571C>T|p.?|187/7028|-8/5451||-5571|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2667C>T|p.?|100/3682|81/2280||2667|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2667C>T|p.?|188/3696|81/2100||2667|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2667C>T|p.?|194/7151|81/5655||2667|-1|	GT:AD:DP:GQ	0/1:15,13:28:48
+17	41270666	.	C	A	.	.	clinvar_vcv=VCV000209552.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2870G>T|p.?|194/7088|81/5592||2870|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5368G>T|p.?|187/7028|-8/5451||-5368|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2870G>T|p.?|100/3682|81/2280||2870|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2870G>T|p.?|188/3696|81/2100||2870|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2870G>T|p.?|194/7151|81/5655||2870|-1|	GT:AD:DP:GQ	0/1:11,4:15:43
+17	41270778	.	C	CT	.	.	clinvar_vcv=VCV000264797.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2983_81-2982insA|p.?|194/7088|81/5592||2983|-1|,CT|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5255_-8+5256insA|p.?|187/7028|-8/5451||-5256|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2983_81-2982insA|p.?|100/3682|81/2280||2983|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2983_81-2982insA|p.?|188/3696|81/2100||2983|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2983_81-2982insA|p.?|194/7151|81/5655||2983|-1|	GT:AD:DP:GQ	0/1:11,5:16:14
+17	41271293	.	GA	G	.	.	ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-3498del|p.?|194/7088|81/5592||3498|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+4740del|p.?|187/7028|-8/5451||-4740|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-3498del|p.?|100/3682|81/2280||3498|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-3498del|p.?|188/3696|81/2100||3498|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-3498del|p.?|194/7151|81/5655||3498|-1|	GT:AD:DP:GQ	0/1:10,10:20:48
+17	41273095	.	G	A	.	.	clinvar_vcv=VCV000209559.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2939C>T|p.?|193/7088|80/5592||-2939|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2939C>T|p.?|187/7028|-8/5451||-2939|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2939C>T|p.?|99/3682|80/2280||-2939|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2939C>T|p.?|187/3696|80/2100||-2939|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2939C>T|p.?|193/7151|80/5655||-2939|-1|	GT:AD:DP:GQ	0/1:12,8:20:47
+17	41273348	.	T	C	.	.	clinvar_vcv=VCV000209561.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2686A>G|p.?|193/7088|80/5592||-2686|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2686A>G|p.?|187/7028|-8/5451||-2686|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2686A>G|p.?|99/3682|80/2280||-2686|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2686A>G|p.?|187/3696|80/2100||-2686|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2686A>G|p.?|193/7151|80/5655||-2686|-1|	GT:AD:DP:GQ	0/1:18,13:31:47
+17	41273379	.	G	C	.	.	clinvar_vcv=VCV000209562.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2655C>G|p.?|193/7088|80/5592||-2655|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2655C>G|p.?|187/7028|-8/5451||-2655|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2655C>G|p.?|99/3682|80/2280||-2655|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2655C>G|p.?|187/3696|80/2100||-2655|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2655C>G|p.?|193/7151|80/5655||-2655|-1|	GT:AD:DP:GQ	0/1:19,14:33:47
+17	41273537	.	A	C	.	.	clinvar_vcv=VCV000209564.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2497T>G|p.?|193/7088|80/5592||-2497|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2497T>G|p.?|187/7028|-8/5451||-2497|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2497T>G|p.?|99/3682|80/2280||-2497|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2497T>G|p.?|187/3696|80/2100||-2497|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2497T>G|p.?|193/7151|80/5655||-2497|-1|	GT:AD:DP:GQ	0/1:14,19:33:48
+17	41274778	.	G	A	.	.	clinvar_vcv=VCV000209565.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+1256C>T|p.?|193/7088|80/5592||-1256|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1256C>T|p.?|187/7028|-8/5451||-1256|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+1256C>T|p.?|99/3682|80/2280||-1256|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1256C>T|p.?|187/3696|80/2100||-1256|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1256C>T|p.?|193/7151|80/5655||-1256|-1|	GT:AD:DP:GQ	0/1:11,16:27:48
+17	41274906	.	G	A	.	.	clinvar_vcv=VCV000209568.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+1128C>T|p.?|193/7088|80/5592||-1128|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1128C>T|p.?|187/7028|-8/5451||-1128|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+1128C>T|p.?|99/3682|80/2280||-1128|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1128C>T|p.?|187/3696|80/2100||-1128|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1128C>T|p.?|193/7151|80/5655||-1128|-1|	GT:AD:DP:GQ	0/1:17,10:27:47
+17	41275081	.	G	GA	.	.	clinvar_vcv=VCV000209569.2;clinvar_germline_classification=Benign;ANN=GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+952_80+953insT|p.?|193/7088|80/5592||-953|-1|,GA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+952_-8+953insT|p.?|187/7028|-8/5451||-953|-1|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+952_80+953insT|p.?|99/3682|80/2280||-953|-1|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+952_80+953insT|p.?|187/3696|80/2100||-953|-1|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+952_80+953insT|p.?|193/7151|80/5655||-953|-1|	GT:AD:DP:GQ	0/1:10,12:22:47
+17	41275151	.	G	C	.	.	clinvar_vcv=VCV000209570.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+883C>G|p.?|193/7088|80/5592||-883|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+883C>G|p.?|187/7028|-8/5451||-883|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+883C>G|p.?|99/3682|80/2280||-883|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+883C>G|p.?|187/3696|80/2100||-883|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+883C>G|p.?|193/7151|80/5655||-883|-1|	GT:AD:DP:GQ	0/1:15,13:28:48
+17	41275366	.	GTTTTTTT	G	.	.	ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+661_80+667del|p.?|193/7088|80/5592||-661|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+661_-8+667del|p.?|187/7028|-8/5451||-661|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+661_80+667del|p.?|99/3682|80/2280||-661|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+661_80+667del|p.?|187/3696|80/2100||-661|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+661_80+667del|p.?|193/7151|80/5655||-661|-1|	GT:AD:DP:GQ	0/1:10,11:21:48
+17	41275645	.	A	G	.	.	clinvar_vcv=VCV000209571.3;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+389T>C|p.?|193/7088|80/5592||-389|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+389T>C|p.?|187/7028|-8/5451||-389|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+389T>C|p.?|99/3682|80/2280||-389|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+389T>C|p.?|187/3696|80/2100||-389|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+389T>C|p.?|193/7151|80/5655||-389|-1|	GT:AD:DP:GQ	0/1:15,17:32:48
+17	41276247	.	A	G	.	.	gnomad_exomes_an=31318;gnomad_exomes_hom=1611;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125468.4;clinvar_germline_classification=Benign;ANN=G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-19-115T>C|p.?|95/7088|-19/5592||115|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-115T>C|p.?|89/7028|-106/5451||115|-1|,G|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||115|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-115T>C|p.?|89/3696|-19/2100||115|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-115T>C|p.?|95/7151|-19/5655||115|-1|	GT:AD:DP:GQ	0/1:18,10:28:44
+17	41276348	.	T	C	.	.	clinvar_vcv=VCV000209574.3;clinvar_germline_classification=Benign;ANN=C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-19-216A>G|p.?|95/7088|-19/5592||216|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-216A>G|p.?|89/7028|-106/5451||216|-1|,C|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||216|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-216A>G|p.?|89/3696|-19/2100||216|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-216A>G|p.?|95/7151|-19/5655||216|-1|	GT:AD:DP:GQ	0/1:17,13:30:47
+17	41277187	.	G	C	.	.	gnomad_exomes_an=29432;gnomad_exomes_hom=4088;gnomad_exomes_het=6345;gnomad_genomes_an=128296;gnomad_genomes_hom=11705;gnomad_genomes_het=29182;clinvar_vcv=VCV000189123.4;clinvar_germline_classification=Benign;ANN=C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-20+101C>G|p.?|94/7088|-20/5592||-101|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-107+107C>G|p.?|88/7028|-107/5451||-107|-1|,C|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||1055|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-20+107C>G|p.?|88/3696|-20/2100||-107|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-20+101C>G|p.?|94/7151|-20/5655||-101|-1|	GT:AD:DP:GQ	0/1:14,14:28:48
 MT	152	.	T	C	.	.	.	GT:GQ:AD:DP	1/1:98:2,10582:10584
 MT	263	.	A	G	.	.	clinvar_vcv=VCV000441147.1;clinvar_germline_classification=not provided	GT:GQ:AD:DP	1/1:98:0,7628:7628
 MT	302	.	A	AC	.	.	.	GT:GQ:AD:DP	1/1:97:40,3496:3536
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@clair3_glnexus_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@clair3_glnexus_vcf.snap
index e6e6b144..78690870 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@clair3_glnexus_vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@clair3_glnexus_vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap
index c90e9563..e41acbb1 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,5 +57,5 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.4, HW: 07.021.624">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64delT|p.?|554/7088|441/5592||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64delT|p.?|460/3682|441/2280||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||-64|	GT:AD:DP:GQ:PS	0|1:11,6:17:43:41256074
+17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64del|p.?|554/7088|441/5592||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64del|p.?|494/7028|300/5451||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64del|p.?|460/3682|441/2280||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64del|p.?|548/3696|441/2100||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64del|p.?|554/7151|441/5655||-64|-1|	GT:AD:DP:GQ:PS	0|1:11,6:17:43:41256074
 MT	750	.	A	G	.	.	clinvar_vcv=VCV000441148.2;clinvar_germline_classification=association not found	GT:GQ:AD:DP	1/1:98:1,7818:7819
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap
index 4e52d004..19e2bb87 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,5 +57,5 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.9, HW: 07.021.624">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CASE
-17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64delT|p.?|554/7088|441/5592||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64delT|p.?|460/3682|441/2280||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||-64|	GT:AD:DP:GQ:PS	0|1:18,14:32:47:41256074
+17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64del|p.?|554/7088|441/5592||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64del|p.?|494/7028|300/5451||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64del|p.?|460/3682|441/2280||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64del|p.?|548/3696|441/2100||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64del|p.?|554/7151|441/5655||-64|-1|	GT:AD:DP:GQ:PS	0|1:18,14:32:47:41256074
 MT	750	.	A	G	.	.	clinvar_vcv=VCV000441148.2;clinvar_germline_classification=association not found	GT:GQ:AD:DP	1/1:98:1,5607:5608
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap
index e3de4dd7..6c094cf3 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -57,5 +61,5 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-17	41210126	.	C	CTAGCACTT	.	.	ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||975|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||975|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|17/21|c.1882-975_1882-974insAAGTGCTA|p.?|1901/3682|1882/2280||975|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||975|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||975|	GT:AD:DP:GQ	0/0:29,0:29:87	0/1:23,13:36:99	0/1:15,17:32:99
+17	41210126	.	C	CTAGCACTT	.	.	ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||975|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||975|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|17/21|c.1882-975_1882-974insAAGTGCTA|p.?|1901/3682|1882/2280||975|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||975|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||975|-1|	GT:AD:DP:GQ	0/0:29,0:29:87	0/1:23,13:36:99	0/1:15,17:32:99
 MT	750	.	A	G	.	.	clinvar_vcv=VCV000441148.2;clinvar_germline_classification=association not found	GT:AD:DP:GQ	1/1:0,2757:2757:99	1/1:0,2392:2392:99	1/1:0,1621:1621:99
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap
index 55ce4ffd..3b79d0e2 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,5 +57,5 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="4.4.0.0">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CASE
-17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64delT|p.?|554/7088|441/5592||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64delT|p.?|460/3682|441/2280||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||-64|	GT:AD:DP:GQ:PS	1|1:0,80:80:99:41256074
+17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64del|p.?|554/7088|441/5592||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64del|p.?|494/7028|300/5451||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64del|p.?|460/3682|441/2280||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64del|p.?|548/3696|441/2100||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64del|p.?|554/7151|441/5655||-64|-1|	GT:AD:DP:GQ:PS	1|1:0,80:80:99:41256074
 MT	750	.	A	G	.	.	clinvar_vcv=VCV000441148.2;clinvar_germline_classification=association not found	GT:AD:DP:GQ	1/1:0,35:35:99
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap
index 73da644f..2efcfb24 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap
@@ -3,552 +3,567 @@ source: src/seqvars/ingest/mod.rs
 expression: "String::from_utf8_lossy(&buffer)"
 ---
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diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@Case_1_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@Case_1_vcf.snap
index 5740a767..990e0508 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@Case_1_vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@Case_1_vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -57,16 +61,16 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father	Case_1_index	Case_1_mother
-17	41249263	.	G	A	.	.	gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_vcv=VCV000055642.108;clinvar_germline_classification=Benign;ANN=A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/23|c.591C>T|p.C197=|704/7088|591/5592|197/1864|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.C150=|644/7028|450/5451|150/1817|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/22|c.591C>T|p.C197=|610/3682|591/2280|197/760|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.C197=|698/3696|591/2100|197/700|0|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.C197=|704/7151|591/5655|197/1885|0|	GT:AD:DP:GQ	0/0:52,0:52:99	0/0:46,0:46:99	0/1:21,21:42:99
-17	41252332	.	T	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-435A>G|p.?|555/7088|442/5592||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-435A>G|p.?|461/3682|442/2280||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||435|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||435|	GT:AD:DP:GQ	0/0:25,0:25:75	0/1:14,14:28:99	0/1:19,21:40:99
-17	41252691	.	ATATAAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-795delATTATA|p.?|555/7088|442/5592||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795delATTATA|p.?|495/7028|301/5451||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-795delATTATA|p.?|461/3682|442/2280||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795delATTATA|p.?|549/3696|442/2100||795|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795delATTATA|p.?|555/7151|442/5655||795|	GT:AD:DP:GQ	0/0:9,0:9:27	0/1:4,10:14:99	0/1:12,11:23:99
-17	41252693	.	ATAAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-797delATTA|p.?|555/7088|442/5592||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797delATTA|p.?|495/7028|301/5451||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-797delATTA|p.?|461/3682|442/2280||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797delATTA|p.?|549/3696|442/2100||797|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797delATTA|p.?|555/7151|442/5655||797|	GT:AD:DP:GQ	0/0:9,0:9:27	0/0:14,0:14:42	0/1:11,11:22:99
-17	41252695	.	AAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-799delAT|p.?|555/7088|442/5592||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799delAT|p.?|495/7028|301/5451||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-799delAT|p.?|461/3682|442/2280||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799delAT|p.?|549/3696|442/2100||799|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799delAT|p.?|555/7151|442/5655||799|	GT:AD:DP:GQ	0/1:3,6:9:79	0/0:14,0:14:42	0/0:22,0:22:66
-17	41252696	.	A	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-799T>A|p.?|555/7088|442/5592||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-799T>A|p.?|461/3682|442/2280||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||799|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||799|	GT:AD:DP:GQ	0/1:6,3:9:78	0/1:10,4:14:98	0/0:22,0:22:67
-17	41252697	.	A	AT	.	.	ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insA|p.?|461/3682|442/2280||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||801|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||801|	GT:AD:DP:GQ	1/1:0,45:45:99	1/0:16,17:33:99	1/0:22,11:33:99
-17	41252697	.	A	ATT	.	.	ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insAA|p.?|461/3682|442/2280||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||801|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||801|	GT:AD:DP:GQ	0/0:45,0:45:99	0/1:17,16:33:99	0/1:12,21:33:99
-17	41254393	.	G	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1746C>A|p.?|554/7088|441/5592||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1746C>A|p.?|460/3682|441/2280||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||-1746|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||-1746|	GT:AD:DP:GQ	0/1:29,8:37:66	./.:.:.:.	0/0:32,3:35:47
-17	41273700	.	C	CA	.	.	ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||-2334|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||-2334|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2333_80+2334insT|p.?|99/3682|80/2280||-2334|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||-2334|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||-2334|	GT:AD:DP:GQ	0/0:14,0:14:42	0/0:6,1:7:10	0/1:5,5:10:65
+17	41249263	.	G	A	.	.	gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_vcv=VCV000055642.108;clinvar_germline_classification=Benign;ANN=A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/23|c.591C>T|p.Cys197=|704/7088|591/5592|197/1864|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.Cys150=|644/7028|450/5451|150/1817|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/22|c.591C>T|p.Cys197=|610/3682|591/2280|197/760|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.Cys197=|698/3696|591/2100|197/700|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.Cys197=|704/7151|591/5655|197/1885|0|-1|	GT:AD:DP:GQ	0/0:52,0:52:99	0/0:46,0:46:99	0/1:21,21:42:99
+17	41252332	.	T	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-435A>G|p.?|555/7088|442/5592||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-435A>G|p.?|461/3682|442/2280||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||435|-1|	GT:AD:DP:GQ	0/0:25,0:25:75	0/1:14,14:28:99	0/1:19,21:40:99
+17	41252691	.	ATATAAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-795del|p.?|555/7088|442/5592||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795del|p.?|495/7028|301/5451||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-795del|p.?|461/3682|442/2280||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795del|p.?|549/3696|442/2100||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795del|p.?|555/7151|442/5655||795|-1|	GT:AD:DP:GQ	0/0:9,0:9:27	0/1:4,10:14:99	0/1:12,11:23:99
+17	41252693	.	ATAAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-797del|p.?|555/7088|442/5592||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797del|p.?|495/7028|301/5451||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-797del|p.?|461/3682|442/2280||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797del|p.?|549/3696|442/2100||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797del|p.?|555/7151|442/5655||797|-1|	GT:AD:DP:GQ	0/0:9,0:9:27	0/0:14,0:14:42	0/1:11,11:22:99
+17	41252695	.	AAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-799del|p.?|555/7088|442/5592||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799del|p.?|495/7028|301/5451||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-799del|p.?|461/3682|442/2280||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799del|p.?|549/3696|442/2100||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799del|p.?|555/7151|442/5655||799|-1|	GT:AD:DP:GQ	0/1:3,6:9:79	0/0:14,0:14:42	0/0:22,0:22:66
+17	41252696	.	A	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-799T>A|p.?|555/7088|442/5592||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-799T>A|p.?|461/3682|442/2280||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||799|-1|	GT:AD:DP:GQ	0/1:6,3:9:78	0/1:10,4:14:98	0/0:22,0:22:67
+17	41252697	.	A	AT	.	.	ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insA|p.?|461/3682|442/2280||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||801|-1|	GT:AD:DP:GQ	1/1:0,45:45:99	1/0:16,17:33:99	1/0:22,11:33:99
+17	41252697	.	A	ATT	.	.	ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insAA|p.?|461/3682|442/2280||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||801|-1|	GT:AD:DP:GQ	0/0:45,0:45:99	0/1:17,16:33:99	0/1:12,21:33:99
+17	41254393	.	G	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1746C>A|p.?|554/7088|441/5592||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1746C>A|p.?|460/3682|441/2280||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||-1746|-1|	GT:AD:DP:GQ	0/1:29,8:37:66	./.:.:.:.	0/0:32,3:35:47
+17	41273700	.	C	CA	.	.	ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||-2334|-1|,CA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||-2334|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2333_80+2334insT|p.?|99/3682|80/2280||-2334|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||-2334|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||-2334|-1|	GT:AD:DP:GQ	0/0:14,0:14:42	0/0:6,1:7:10	0/1:5,5:10:65
 MT	73	.	A	G	.	.	clinvar_vcv=VCV003066071.1;clinvar_germline_classification=Affects	GT:AD:DP:GQ	0/0:3975,0:3975:99	1/1:0,2871:2871:99	1/1:0,3320:3320:99
 MT	119	.	T	C	.	.	.	GT:AD:DP:GQ	0/0:5417,1:5418:99	1/1:0,4039:4039:99	1/1:1,4112:4113:99
 MT	189	.	A	G	.	.	.	GT:AD:DP:GQ	0/0:3069,0:3069:99	1/1:0,1721:1721:99	1/1:0,2204:2204:99
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@NA12878_dragen_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@NA12878_dragen_vcf.snap
index 0f4c1039..f8a5b162 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@NA12878_dragen_vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_with_id_map@NA12878_dragen_vcf.snap
@@ -11,10 +11,14 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,85 +57,85 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.4, HW: 07.021.624">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	my-custom-id
-17	41244000	.	T	C	.	.	gnomad_exomes_an=31346;gnomad_exomes_hom=1591;gnomad_exomes_het=6707;gnomad_genomes_an=250954;gnomad_genomes_hom=16402;gnomad_genomes_het=55703;clinvar_vcv=VCV000041818.87;clinvar_germline_classification=Benign;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.3548A>G|p.K1183R|3661/7088|3548/5592|1183/1864|0|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.3407A>G|p.K1136R|3601/7028|3407/5451|1136/1817|0|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.788-951A>G|p.?|807/3682|788/2280||951|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-951A>G|p.?|895/3696|788/2100||951|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3548A>G|p.K1183R|3661/7151|3548/5655|1183/1885|0|	GT:AD:DP:GQ	0/1:8,18:26:43
-17	41244435	.	T	C	.	.	gnomad_exomes_an=31332;gnomad_exomes_hom=1505;gnomad_exomes_het=6415;gnomad_genomes_an=251032;gnomad_genomes_hom=16145;gnomad_genomes_het=55137;clinvar_vcv=VCV000041815.87;clinvar_germline_classification=Benign;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.3113A>G|p.E1038G|3226/7088|3113/5592|1038/1864|0|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2972A>G|p.E991G|3166/7028|2972/5451|991/1817|0|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.788-1386A>G|p.?|807/3682|788/2280||1386|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-1386A>G|p.?|895/3696|788/2100||1386|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3113A>G|p.E1038G|3226/7151|3113/5655|1038/1885|0|	GT:AD:DP:GQ	0/1:12,14:26:47
-17	41244936	.	G	A	.	.	gnomad_exomes_an=31324;gnomad_exomes_hom=4287;gnomad_exomes_het=6594;gnomad_genomes_an=251034;gnomad_genomes_hom=22738;gnomad_genomes_het=55898;clinvar_vcv=VCV000041812.88;clinvar_germline_classification=Benign;ANN=A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2612C>T|p.P871L|2725/7088|2612/5592|871/1864|0|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2471C>T|p.P824L|2665/7028|2471/5451|824/1817|0|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1825C>T|p.?|806/3682|787/2280||-1825|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1825C>T|p.?|894/3696|787/2100||-1825|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2612C>T|p.P871L|2725/7151|2612/5655|871/1885|0|	GT:AD:DP:GQ	0/1:17,13:30:47
-17	41245237	.	A	G	.	.	gnomad_exomes_an=31314;gnomad_exomes_hom=1492;gnomad_exomes_het=6416;gnomad_genomes_an=250946;gnomad_genomes_hom=16057;gnomad_genomes_het=55063;clinvar_vcv=VCV000125554.83;clinvar_germline_classification=Benign;ANN=G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2311T>C|p.L771=|2424/7088|2311/5592|771/1864|0|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2170T>C|p.L724=|2364/7028|2170/5451|724/1817|0|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1524T>C|p.?|806/3682|787/2280||-1524|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1524T>C|p.?|894/3696|787/2100||-1524|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2311T>C|p.L771=|2424/7151|2311/5655|771/1885|0|	GT:AD:DP:GQ	0/1:18,11:29:46
-17	41245466	.	G	A	.	.	gnomad_exomes_an=31338;gnomad_exomes_hom=1602;gnomad_exomes_het=6709;gnomad_genomes_an=251110;gnomad_genomes_hom=16420;gnomad_genomes_het=55707;clinvar_vcv=VCV000125536.84;clinvar_germline_classification=Benign;ANN=A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2082C>T|p.S694=|2195/7088|2082/5592|694/1864|0|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.1941C>T|p.S647=|2135/7028|1941/5451|647/1817|0|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1295C>T|p.?|806/3682|787/2280||-1295|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1295C>T|p.?|894/3696|787/2100||-1295|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2082C>T|p.S694=|2195/7151|2082/5655|694/1885|0|	GT:AD:DP:GQ	0/1:11,8:19:48
-17	41247122	.	A	ACCT	.	.	clinvar_vcv=VCV000127125.5;clinvar_germline_classification=Benign;ANN=ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|9/22|c.671-246_671-245insAGG|p.?|784/7088|671/5592||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.530-246_530-245insAGG|p.?|724/7028|530/5451||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|8/21|c.671-246_671-245insAGG|p.?|690/3682|671/2280||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.671-246_671-245insAGG|p.?|778/3696|671/2100||246|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.671-246_671-245insAGG|p.?|784/7151|671/5655||246|	GT:AD:DP:GQ	0/1:18,11:29:45
-17	41247604	.	A	C	.	.	clinvar_vcv=VCV000209447.5;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|9/22|c.670+259T>G|p.?|783/7088|670/5592||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.529+259T>G|p.?|723/7028|529/5451||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|8/21|c.670+259T>G|p.?|689/3682|670/2280||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.670+259T>G|p.?|777/3696|670/2100||-259|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.670+259T>G|p.?|783/7151|670/5655||-259|	GT:AD:DP:GQ	0/1:12,11:23:47
-17	41248164	.	C	T	.	.	clinvar_vcv=VCV000209449.4;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-225G>A|p.?|707/7088|594/5592||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-225G>A|p.?|647/7028|453/5451||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-225G>A|p.?|613/3682|594/2280||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-225G>A|p.?|701/3696|594/2100||225|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-225G>A|p.?|707/7151|594/5655||225|	GT:AD:DP:GQ	0/1:14,7:21:44
-17	41248393	.	C	CAAAAAAAAAA	.	.	ANN=CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-455_594-454insTTTTTTTTTT|p.?|707/7088|594/5592||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-455_453-454insTTTTTTTTTT|p.?|647/7028|453/5451||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-455_594-454insTTTTTTTTTT|p.?|613/3682|594/2280||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-455_594-454insTTTTTTTTTT|p.?|701/3696|594/2100||455|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-455_594-454insTTTTTTTTTT|p.?|707/7151|594/5655||455|	GT:AD:DP:GQ	0/1:9,7:16:48
-17	41248484	.	G	C	.	.	clinvar_vcv=VCV000209450.4;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-545C>G|p.?|707/7088|594/5592||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-545C>G|p.?|647/7028|453/5451||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-545C>G|p.?|613/3682|594/2280||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-545C>G|p.?|701/3696|594/2100||545|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-545C>G|p.?|707/7151|594/5655||545|	GT:AD:DP:GQ	0/1:11,9:20:48
-17	41248588	.	CA	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-650delT|p.?|707/7088|594/5592||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-650delT|p.?|647/7028|453/5451||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-650delT|p.?|613/3682|594/2280||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-650delT|p.?|701/3696|594/2100||650|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-650delT|p.?|707/7151|594/5655||650|	GT:AD:DP:GQ	0/1:9,10:19:42
-17	41249094	.	A	G	.	.	gnomad_exomes_an=31332;gnomad_exomes_hom=1602;gnomad_exomes_het=6703;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000209451.5;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.593+167T>C|p.?|706/7088|593/5592||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.452+167T>C|p.?|646/7028|452/5451||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.593+167T>C|p.?|612/3682|593/2280||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.593+167T>C|p.?|700/3696|593/2100||-167|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.593+167T>C|p.?|706/7151|593/5655||-167|	GT:AD:DP:GQ	0/1:9,7:16:48
-17	41249363	.	TA	T	.	.	gnomad_exomes_an=31286;gnomad_exomes_hom=1497;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.548-58delT|p.?|661/7088|548/5592||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-58delT|p.?|601/7028|407/5451||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.548-58delT|p.?|567/3682|548/2280||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-58delT|p.?|655/3696|548/2100||58|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-58delT|p.?|661/7151|548/5655||58|	GT:AD:DP:GQ	0/1:12,13:25:48
-17	41250047	.	C	CT	.	.	ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.548-742_548-741insA|p.?|661/7088|548/5592||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-742_407-741insA|p.?|601/7028|407/5451||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.548-742_548-741insA|p.?|567/3682|548/2280||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-742_548-741insA|p.?|655/3696|548/2100||742|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-742_548-741insA|p.?|661/7151|548/5655||742|	GT:AD:DP:GQ	0/1:13,7:20:18
-17	41250678	.	C	CT	.	.	clinvar_vcv=VCV000209458.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+1113_547+1114insA|p.?|660/7088|547/5592||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+1113_406+1114insA|p.?|600/7028|406/5451||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+1113_547+1114insA|p.?|566/3682|547/2280||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+1113_547+1114insA|p.?|654/3696|547/2100||-1114|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+1113_547+1114insA|p.?|660/7151|547/5655||-1114|	GT:AD:DP:GQ	0/1:6,16:22:42
-17	41250923	.	T	C	.	.	clinvar_vcv=VCV000209460.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+869A>G|p.?|660/7088|547/5592||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+869A>G|p.?|600/7028|406/5451||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+869A>G|p.?|566/3682|547/2280||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+869A>G|p.?|654/3696|547/2100||-869|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+869A>G|p.?|660/7151|547/5655||-869|	GT:AD:DP:GQ	0/1:13,9:22:47
-17	41251495	.	C	G	.	.	clinvar_vcv=VCV000209463.4;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+297G>C|p.?|660/7088|547/5592||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+297G>C|p.?|600/7028|406/5451||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+297G>C|p.?|566/3682|547/2280||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+297G>C|p.?|654/3696|547/2100||-297|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+297G>C|p.?|660/7151|547/5655||-297|	GT:AD:DP:GQ	0/1:11,15:26:48
-17	41251646	.	T	A	.	.	gnomad_exomes_an=31294;gnomad_exomes_hom=1592;gnomad_exomes_het=6693;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125879.7;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+146A>T|p.?|660/7088|547/5592||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+146A>T|p.?|600/7028|406/5451||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+146A>T|p.?|566/3682|547/2280||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+146A>T|p.?|654/3696|547/2100||-146|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+146A>T|p.?|660/7151|547/5655||-146|	GT:AD:DP:GQ	0/1:11,8:19:48
-17	41252575	.	G	A	.	.	clinvar_vcv=VCV000209466.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-678C>T|p.?|555/7088|442/5592||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-678C>T|p.?|495/7028|301/5451||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-678C>T|p.?|461/3682|442/2280||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-678C>T|p.?|549/3696|442/2100||678|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-678C>T|p.?|555/7151|442/5655||678|	GT:AD:DP:GQ:PS	1|1:0,3:3:5:41252575
-17	41252591	.	C	CAT	.	.	clinvar_vcv=VCV000264796.2;clinvar_germline_classification=Benign;ANN=CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-695_442-694insAT|p.?|555/7088|442/5592||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-695_301-694insAT|p.?|495/7028|301/5451||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-695_442-694insAT|p.?|461/3682|442/2280||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-695_442-694insAT|p.?|549/3696|442/2100||695|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-695_442-694insAT|p.?|555/7151|442/5655||695|	GT:AD:DP:GQ:PS	1|1:0,2:2:4:41252575
-17	41254174	.	A	G	.	.	clinvar_vcv=VCV000209478.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1965T>C|p.?|554/7088|441/5592||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1965T>C|p.?|494/7028|300/5451||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1965T>C|p.?|460/3682|441/2280||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1965T>C|p.?|548/3696|441/2100||-1965|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1965T>C|p.?|554/7151|441/5655||-1965|	GT:AD:DP:GQ	0/1:14,13:27:48
-17	41254374	.	C	CTTTTTTTT	.	.	ANN=CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1764_441+1765insAAAAAAAA|p.?|554/7088|441/5592||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1764_300+1765insAAAAAAAA|p.?|494/7028|300/5451||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1764_441+1765insAAAAAAAA|p.?|460/3682|441/2280||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1764_441+1765insAAAAAAAA|p.?|548/3696|441/2100||-1765|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1764_441+1765insAAAAAAAA|p.?|554/7151|441/5655||-1765|	GT:AD:DP:GQ	0/1:6,7:13:48
-17	41254405	.	C	T	.	.	clinvar_vcv=VCV000264778.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1734G>A|p.?|554/7088|441/5592||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1734G>A|p.?|494/7028|300/5451||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1734G>A|p.?|460/3682|441/2280||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1734G>A|p.?|548/3696|441/2100||-1734|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1734G>A|p.?|554/7151|441/5655||-1734|	GT:AD:DP:GQ	0/1:5,9:14:43
-17	41254486	.	T	G	.	.	clinvar_vcv=VCV000209479.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1653A>C|p.?|554/7088|441/5592||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1653A>C|p.?|494/7028|300/5451||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1653A>C|p.?|460/3682|441/2280||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1653A>C|p.?|548/3696|441/2100||-1653|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1653A>C|p.?|554/7151|441/5655||-1653|	GT:AD:DP:GQ	0/1:8,15:23:46
-17	41254965	.	C	CT	.	.	clinvar_vcv=VCV000264845.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1173_441+1174insA|p.?|554/7088|441/5592||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1173_300+1174insA|p.?|494/7028|300/5451||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1173_441+1174insA|p.?|460/3682|441/2280||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1173_441+1174insA|p.?|548/3696|441/2100||-1174|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1173_441+1174insA|p.?|554/7151|441/5655||-1174|	GT:AD:DP:GQ	0/1:14,8:22:22
-17	41255102	.	A	G	.	.	clinvar_vcv=VCV000209483.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1037T>C|p.?|554/7088|441/5592||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1037T>C|p.?|494/7028|300/5451||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1037T>C|p.?|460/3682|441/2280||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1037T>C|p.?|548/3696|441/2100||-1037|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1037T>C|p.?|554/7151|441/5655||-1037|	GT:AD:DP:GQ:PS	0|1:19,12:31:46:41255102
-17	41255111	.	A	T	.	.	clinvar_vcv=VCV000209484.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1028T>A|p.?|554/7088|441/5592||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1028T>A|p.?|494/7028|300/5451||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1028T>A|p.?|460/3682|441/2280||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1028T>A|p.?|548/3696|441/2100||-1028|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1028T>A|p.?|554/7151|441/5655||-1028|	GT:AD:DP:GQ:PS	0|1:19,12:31:46:41255102
-17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64delT|p.?|554/7088|441/5592||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64delT|p.?|460/3682|441/2280||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||-64|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||-64|	GT:AD:DP:GQ:PS	0|1:11,6:17:43:41256074
-17	41256089	.	AAAAAAAAAGAAAAG	A	.	.	gnomad_exomes_an=28388;gnomad_exomes_hom=1079;gnomad_exomes_het=5744;gnomad_genomes_an=167932;gnomad_genomes_hom=9911;gnomad_genomes_het=23697;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7088|441/5592||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+36_300+49delCTTTTCTTTTTTTT|p.?|494/7028|300/5451||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|460/3682|441/2280||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|548/3696|441/2100||-36|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7151|441/5655||-36|	GT:AD:DP:GQ:PS	0|1:13,6:19:43:41256074
-17	41257134	.	T	C	.	.	gnomad_exomes_an=31346;gnomad_exomes_hom=4418;gnomad_exomes_het=6505;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125614.7;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.213-161A>G|p.?|326/7088|213/5592||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-161A>G|p.?|266/7028|72/5451||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.213-161A>G|p.?|232/3682|213/2280||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-161A>G|p.?|320/3696|213/2100||161|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-161A>G|p.?|326/7151|213/5655||161|	GT:AD:DP:GQ	0/1:14,15:29:48
-17	41257458	.	A	C	.	.	clinvar_vcv=VCV000209489.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.213-485T>G|p.?|326/7088|213/5592||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-485T>G|p.?|266/7028|72/5451||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.213-485T>G|p.?|232/3682|213/2280||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-485T>G|p.?|320/3696|213/2100||485|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-485T>G|p.?|326/7151|213/5655||485|	GT:AD:DP:GQ	0/1:11,15:26:48
-17	41258043	.	C	T	.	.	clinvar_vcv=VCV000209491.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.212+430G>A|p.?|325/7088|212/5592||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+430G>A|p.?|265/7028|71/5451||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.212+430G>A|p.?|231/3682|212/2280||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+430G>A|p.?|319/3696|212/2100||-430|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+430G>A|p.?|325/7151|212/5655||-430|	GT:AD:DP:GQ	0/1:14,13:27:48
-17	41258135	.	T	TA	.	.	ANN=TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.212+337_212+338insT|p.?|325/7088|212/5592||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+337_71+338insT|p.?|265/7028|71/5451||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.212+337_212+338insT|p.?|231/3682|212/2280||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+337_212+338insT|p.?|319/3696|212/2100||-338|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+337_212+338insT|p.?|325/7151|212/5655||-338|	GT:AD:DP:GQ	1/1:3,11:14:4
-17	41259049	.	C	T	.	.	clinvar_vcv=VCV000209494.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-499G>A|p.?|248/7088|135/5592||499|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-499G>A|p.?|188/7028|-7/5451||499|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-499G>A|p.?|154/3682|135/2280||499|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-499G>A|p.?|242/3696|135/2100||499|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-499G>A|p.?|248/7151|135/5655||499|	GT:AD:DP:GQ	0/1:8,8:16:48
-17	41259079	.	A	ATT	.	.	ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-530_135-529insAA|p.?|248/7088|135/5592||530|,ATT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-530_-7-529insAA|p.?|188/7028|-7/5451||530|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-530_135-529insAA|p.?|154/3682|135/2280||530|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-530_135-529insAA|p.?|242/3696|135/2100||530|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-530_135-529insAA|p.?|248/7151|135/5655||530|	GT:AD:DP:GQ	0/1:10,3:13:7
-17	41259113	.	G	A	.	.	clinvar_vcv=VCV000264811.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-563C>T|p.?|248/7088|135/5592||563|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-563C>T|p.?|188/7028|-7/5451||563|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-563C>T|p.?|154/3682|135/2280||563|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-563C>T|p.?|242/3696|135/2100||563|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-563C>T|p.?|248/7151|135/5655||563|	GT:AD:DP:GQ	0/1:11,8:19:48
-17	41260352	.	C	CA	.	.	clinvar_vcv=VCV000264791.2;clinvar_germline_classification=Benign;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-1803_135-1802insT|p.?|248/7088|135/5592||1803|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-1803_-7-1802insT|p.?|188/7028|-7/5451||1803|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-1803_135-1802insT|p.?|154/3682|135/2280||1803|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-1803_135-1802insT|p.?|242/3696|135/2100||1803|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-1803_135-1802insT|p.?|248/7151|135/5655||1803|	GT:AD:DP:GQ	0/1:11,8:19:43
-17	41260723	.	C	CAAAAA	.	.	ANN=CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2174_135-2173insTTTTT|p.?|248/7088|135/5592||2174|,CAAAAA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2174_-7-2173insTTTTT|p.?|188/7028|-7/5451||2174|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2174_135-2173insTTTTT|p.?|154/3682|135/2280||2174|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2174_135-2173insTTTTT|p.?|242/3696|135/2100||2174|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2174_135-2173insTTTTT|p.?|248/7151|135/5655||2174|	GT:AD:DP:GQ	0/1:1,1:2:20
-17	41260808	.	A	G	.	.	clinvar_vcv=VCV000209499.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2258T>C|p.?|248/7088|135/5592||2258|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2258T>C|p.?|188/7028|-7/5451||2258|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2258T>C|p.?|154/3682|135/2280||2258|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2258T>C|p.?|242/3696|135/2100||2258|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2258T>C|p.?|248/7151|135/5655||2258|	GT:AD:DP:GQ	0/1:12,3:15:32
-17	41261058	.	T	TCTATCTATCTACCTAC	.	.	clinvar_vcv=VCV000264813.2;clinvar_germline_classification=Benign;ANN=TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7088|135/5592||2509|,TCTATCTATCTACCTAC|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2509_-7-2508insGTAGGTAGATAGATAG|p.?|188/7028|-7/5451||2509|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|154/3682|135/2280||2509|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|242/3696|135/2100||2509|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7151|135/5655||2509|	GT:AD:DP:GQ	0/1:9,11:20:48
-17	41261233	.	C	T	.	.	clinvar_vcv=VCV000209503.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2683G>A|p.?|248/7088|135/5592||2683|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2683G>A|p.?|188/7028|-7/5451||2683|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2683G>A|p.?|154/3682|135/2280||2683|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2683G>A|p.?|242/3696|135/2100||2683|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2683G>A|p.?|248/7151|135/5655||2683|	GT:AD:DP:GQ	0/1:12,15:27:48
-17	41263044	.	A	G	.	.	clinvar_vcv=VCV000209512.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-4494T>C|p.?|248/7088|135/5592||4494|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4494T>C|p.?|188/7028|-7/5451||4494|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-4494T>C|p.?|154/3682|135/2280||4494|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4494T>C|p.?|242/3696|135/2100||4494|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4494T>C|p.?|248/7151|135/5655||4494|	GT:AD:DP:GQ	0/1:7,7:14:48
-17	41263117	.	C	CA	.	.	ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-4568_135-4567insT|p.?|248/7088|135/5592||4568|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4568_-7-4567insT|p.?|188/7028|-7/5451||4568|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-4568_135-4567insT|p.?|154/3682|135/2280||4568|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4568_135-4567insT|p.?|242/3696|135/2100||4568|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4568_135-4567insT|p.?|248/7151|135/5655||4568|	GT:AD:DP:GQ	0/1:13,10:23:34
-17	41263566	.	T	C	.	.	clinvar_vcv=VCV000209516.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+4177A>G|p.?|247/7088|134/5592||-4177|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5016A>G|p.?|188/7028|-7/5451||5016|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+4177A>G|p.?|153/3682|134/2280||-4177|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+4177A>G|p.?|241/3696|134/2100||-4177|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+4177A>G|p.?|247/7151|134/5655||-4177|	GT:AD:DP:GQ	0/1:11,8:19:48
-17	41264146	.	G	A	.	.	clinvar_vcv=VCV000209519.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3597C>T|p.?|247/7088|134/5592||-3597|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5596C>T|p.?|188/7028|-7/5451||5596|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3597C>T|p.?|153/3682|134/2280||-3597|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3597C>T|p.?|241/3696|134/2100||-3597|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3597C>T|p.?|247/7151|134/5655||-3597|	GT:AD:DP:GQ	0/1:13,7:20:45
-17	41264364	.	A	G	.	.	clinvar_vcv=VCV000209521.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3379T>C|p.?|247/7088|134/5592||-3379|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5814T>C|p.?|188/7028|-7/5451||5814|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3379T>C|p.?|153/3682|134/2280||-3379|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3379T>C|p.?|241/3696|134/2100||-3379|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3379T>C|p.?|247/7151|134/5655||-3379|	GT:AD:DP:GQ	0/1:8,16:24:45
-17	41264739	.	C	T	.	.	clinvar_vcv=VCV000264785.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3004G>A|p.?|247/7088|134/5592||-3004|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6189G>A|p.?|188/7028|-7/5451||6189|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3004G>A|p.?|153/3682|134/2280||-3004|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3004G>A|p.?|241/3696|134/2100||-3004|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3004G>A|p.?|247/7151|134/5655||-3004|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
-17	41264740	.	TGA	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3001_134+3002delTC|p.?|247/7088|134/5592||-3001|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6192_-7-6191delTC|p.?|188/7028|-7/5451||6191|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3001_134+3002delTC|p.?|153/3682|134/2280||-3001|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3001_134+3002delTC|p.?|241/3696|134/2100||-3001|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3001_134+3002delTC|p.?|247/7151|134/5655||-3001|	GT:AD:DP:GQ	0/1:14,16:30:48
-17	41264743	.	CT	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2999delA|p.?|247/7088|134/5592||-2999|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6194delA|p.?|188/7028|-7/5451||6194|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2999delA|p.?|153/3682|134/2280||-2999|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2999delA|p.?|241/3696|134/2100||-2999|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2999delA|p.?|247/7151|134/5655||-2999|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
-17	41264749	.	C	G	.	.	clinvar_vcv=VCV000264823.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2994G>C|p.?|247/7088|134/5592||-2994|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6199G>C|p.?|188/7028|-7/5451||6199|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2994G>C|p.?|153/3682|134/2280||-2994|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2994G>C|p.?|241/3696|134/2100||-2994|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2994G>C|p.?|247/7151|134/5655||-2994|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
-17	41264750	.	A	T	.	.	clinvar_vcv=VCV000264824.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2993T>A|p.?|247/7088|134/5592||-2993|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6200T>A|p.?|188/7028|-7/5451||6200|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2993T>A|p.?|153/3682|134/2280||-2993|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2993T>A|p.?|241/3696|134/2100||-2993|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2993T>A|p.?|247/7151|134/5655||-2993|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
-17	41264751	.	A	AGGG	.	.	ANN=AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2991_134+2992insCCC|p.?|247/7088|134/5592||-2992|,AGGG|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6202_-7-6201insCCC|p.?|188/7028|-7/5451||6202|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2991_134+2992insCCC|p.?|153/3682|134/2280||-2992|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2991_134+2992insCCC|p.?|241/3696|134/2100||-2992|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2991_134+2992insCCC|p.?|247/7151|134/5655||-2992|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
-17	41264753	.	C	T	.	.	clinvar_vcv=VCV000264819.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2990G>A|p.?|247/7088|134/5592||-2990|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6203G>A|p.?|188/7028|-7/5451||6203|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2990G>A|p.?|153/3682|134/2280||-2990|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2990G>A|p.?|241/3696|134/2100||-2990|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2990G>A|p.?|247/7151|134/5655||-2990|	GT:AD:DP:GQ:PS	0|1:14,13:27:48:41264739
-17	41264755	.	TGAAAC	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2983_134+2987delGTTTC|p.?|247/7088|134/5592||-2983|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6210_-7-6206delGTTTC|p.?|188/7028|-7/5451||6206|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2983_134+2987delGTTTC|p.?|153/3682|134/2280||-2983|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2983_134+2987delGTTTC|p.?|241/3696|134/2100||-2983|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2983_134+2987delGTTTC|p.?|247/7151|134/5655||-2983|	GT:AD:DP:GQ:PS	0|1:14,13:27:48:41264739
-17	41265776	.	A	G	.	.	clinvar_vcv=VCV000209524.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+1967T>C|p.?|247/7088|134/5592||-1967|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7226T>C|p.?|188/7028|-7/5451||7226|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+1967T>C|p.?|153/3682|134/2280||-1967|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1967T>C|p.?|241/3696|134/2100||-1967|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1967T>C|p.?|247/7151|134/5655||-1967|	GT:AD:DP:GQ	0/1:23,14:37:44
-17	41266407	.	C	CT	.	.	clinvar_vcv=VCV000264777.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+1335_134+1336insA|p.?|247/7088|134/5592||-1336|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7858_-7-7857insA|p.?|188/7028|-7/5451||7858|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+1335_134+1336insA|p.?|153/3682|134/2280||-1336|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1335_134+1336insA|p.?|241/3696|134/2100||-1336|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1335_134+1336insA|p.?|247/7151|134/5655||-1336|	GT:AD:DP:GQ	0/1:10,8:18:33
-17	41267050	.	G	A	.	.	clinvar_vcv=VCV000209531.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+693C>T|p.?|247/7088|134/5592||-693|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-8500C>T|p.?|188/7028|-7/5451||8500|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+693C>T|p.?|153/3682|134/2280||-693|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+693C>T|p.?|241/3696|134/2100||-693|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+693C>T|p.?|247/7151|134/5655||-693|	GT:AD:DP:GQ	0/1:7,16:23:44
-17	41267518	.	CA	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+224delT|p.?|247/7088|134/5592||-224|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+8515delT|p.?|187/7028|-8/5451||-8515|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+224delT|p.?|153/3682|134/2280||-224|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+224delT|p.?|241/3696|134/2100||-224|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+224delT|p.?|247/7151|134/5655||-224|	GT:AD:DP:GQ	0/1:11,8:19:35
-17	41268206	.	A	C	.	.	clinvar_vcv=VCV000209537.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-410T>G|p.?|194/7088|81/5592||410|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7828T>G|p.?|187/7028|-8/5451||-7828|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-410T>G|p.?|100/3682|81/2280||410|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-410T>G|p.?|188/3696|81/2100||410|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-410T>G|p.?|194/7151|81/5655||410|	GT:AD:DP:GQ:PS	0|1:13,9:22:46:41268206
-17	41268208	.	C	CT	.	.	clinvar_vcv=VCV000264808.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-413_81-412insA|p.?|194/7088|81/5592||413|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7825_-8+7826insA|p.?|187/7028|-8/5451||-7826|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-413_81-412insA|p.?|100/3682|81/2280||413|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-413_81-412insA|p.?|188/3696|81/2100||413|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-413_81-412insA|p.?|194/7151|81/5655||413|	GT:AD:DP:GQ:PS	0|1:13,9:22:46:41268206
-17	41270229	.	T	G	.	.	clinvar_vcv=VCV000209545.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2433A>C|p.?|194/7088|81/5592||2433|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5805A>C|p.?|187/7028|-8/5451||-5805|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2433A>C|p.?|100/3682|81/2280||2433|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2433A>C|p.?|188/3696|81/2100||2433|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2433A>C|p.?|194/7151|81/5655||2433|	GT:AD:DP:GQ	0/1:7,17:24:40
-17	41270277	.	C	T	.	.	clinvar_vcv=VCV000209547.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2481G>A|p.?|194/7088|81/5592||2481|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5757G>A|p.?|187/7028|-8/5451||-5757|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2481G>A|p.?|100/3682|81/2280||2481|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2481G>A|p.?|188/3696|81/2100||2481|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2481G>A|p.?|194/7151|81/5655||2481|	GT:AD:DP:GQ	0/1:9,13:22:48
-17	41270463	.	G	A	.	.	clinvar_vcv=VCV000209551.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2667C>T|p.?|194/7088|81/5592||2667|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5571C>T|p.?|187/7028|-8/5451||-5571|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2667C>T|p.?|100/3682|81/2280||2667|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2667C>T|p.?|188/3696|81/2100||2667|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2667C>T|p.?|194/7151|81/5655||2667|	GT:AD:DP:GQ	0/1:15,13:28:48
-17	41270666	.	C	A	.	.	clinvar_vcv=VCV000209552.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2870G>T|p.?|194/7088|81/5592||2870|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5368G>T|p.?|187/7028|-8/5451||-5368|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2870G>T|p.?|100/3682|81/2280||2870|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2870G>T|p.?|188/3696|81/2100||2870|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2870G>T|p.?|194/7151|81/5655||2870|	GT:AD:DP:GQ	0/1:11,4:15:43
-17	41270778	.	C	CT	.	.	clinvar_vcv=VCV000264797.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2983_81-2982insA|p.?|194/7088|81/5592||2983|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5255_-8+5256insA|p.?|187/7028|-8/5451||-5256|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2983_81-2982insA|p.?|100/3682|81/2280||2983|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2983_81-2982insA|p.?|188/3696|81/2100||2983|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2983_81-2982insA|p.?|194/7151|81/5655||2983|	GT:AD:DP:GQ	0/1:11,5:16:14
-17	41271293	.	GA	G	.	.	ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-3498delT|p.?|194/7088|81/5592||3498|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+4740delT|p.?|187/7028|-8/5451||-4740|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-3498delT|p.?|100/3682|81/2280||3498|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-3498delT|p.?|188/3696|81/2100||3498|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-3498delT|p.?|194/7151|81/5655||3498|	GT:AD:DP:GQ	0/1:10,10:20:48
-17	41273095	.	G	A	.	.	clinvar_vcv=VCV000209559.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2939C>T|p.?|193/7088|80/5592||-2939|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2939C>T|p.?|187/7028|-8/5451||-2939|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2939C>T|p.?|99/3682|80/2280||-2939|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2939C>T|p.?|187/3696|80/2100||-2939|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2939C>T|p.?|193/7151|80/5655||-2939|	GT:AD:DP:GQ	0/1:12,8:20:47
-17	41273348	.	T	C	.	.	clinvar_vcv=VCV000209561.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2686A>G|p.?|193/7088|80/5592||-2686|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2686A>G|p.?|187/7028|-8/5451||-2686|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2686A>G|p.?|99/3682|80/2280||-2686|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2686A>G|p.?|187/3696|80/2100||-2686|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2686A>G|p.?|193/7151|80/5655||-2686|	GT:AD:DP:GQ	0/1:18,13:31:47
-17	41273379	.	G	C	.	.	clinvar_vcv=VCV000209562.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2655C>G|p.?|193/7088|80/5592||-2655|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2655C>G|p.?|187/7028|-8/5451||-2655|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2655C>G|p.?|99/3682|80/2280||-2655|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2655C>G|p.?|187/3696|80/2100||-2655|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2655C>G|p.?|193/7151|80/5655||-2655|	GT:AD:DP:GQ	0/1:19,14:33:47
-17	41273537	.	A	C	.	.	clinvar_vcv=VCV000209564.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2497T>G|p.?|193/7088|80/5592||-2497|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2497T>G|p.?|187/7028|-8/5451||-2497|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2497T>G|p.?|99/3682|80/2280||-2497|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2497T>G|p.?|187/3696|80/2100||-2497|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2497T>G|p.?|193/7151|80/5655||-2497|	GT:AD:DP:GQ	0/1:14,19:33:48
-17	41274778	.	G	A	.	.	clinvar_vcv=VCV000209565.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+1256C>T|p.?|193/7088|80/5592||-1256|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1256C>T|p.?|187/7028|-8/5451||-1256|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+1256C>T|p.?|99/3682|80/2280||-1256|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1256C>T|p.?|187/3696|80/2100||-1256|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1256C>T|p.?|193/7151|80/5655||-1256|	GT:AD:DP:GQ	0/1:11,16:27:48
-17	41274906	.	G	A	.	.	clinvar_vcv=VCV000209568.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+1128C>T|p.?|193/7088|80/5592||-1128|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1128C>T|p.?|187/7028|-8/5451||-1128|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+1128C>T|p.?|99/3682|80/2280||-1128|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1128C>T|p.?|187/3696|80/2100||-1128|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1128C>T|p.?|193/7151|80/5655||-1128|	GT:AD:DP:GQ	0/1:17,10:27:47
-17	41275081	.	G	GA	.	.	clinvar_vcv=VCV000209569.2;clinvar_germline_classification=Benign;ANN=GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+952_80+953insT|p.?|193/7088|80/5592||-953|,GA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+952_-8+953insT|p.?|187/7028|-8/5451||-953|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+952_80+953insT|p.?|99/3682|80/2280||-953|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+952_80+953insT|p.?|187/3696|80/2100||-953|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+952_80+953insT|p.?|193/7151|80/5655||-953|	GT:AD:DP:GQ	0/1:10,12:22:47
-17	41275151	.	G	C	.	.	clinvar_vcv=VCV000209570.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+883C>G|p.?|193/7088|80/5592||-883|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+883C>G|p.?|187/7028|-8/5451||-883|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+883C>G|p.?|99/3682|80/2280||-883|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+883C>G|p.?|187/3696|80/2100||-883|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+883C>G|p.?|193/7151|80/5655||-883|	GT:AD:DP:GQ	0/1:15,13:28:48
-17	41275366	.	GTTTTTTT	G	.	.	ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+661_80+667delAAAAAAA|p.?|193/7088|80/5592||-661|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+661_-8+667delAAAAAAA|p.?|187/7028|-8/5451||-661|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+661_80+667delAAAAAAA|p.?|99/3682|80/2280||-661|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+661_80+667delAAAAAAA|p.?|187/3696|80/2100||-661|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+661_80+667delAAAAAAA|p.?|193/7151|80/5655||-661|	GT:AD:DP:GQ	0/1:10,11:21:48
-17	41275645	.	A	G	.	.	clinvar_vcv=VCV000209571.3;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+389T>C|p.?|193/7088|80/5592||-389|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+389T>C|p.?|187/7028|-8/5451||-389|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+389T>C|p.?|99/3682|80/2280||-389|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+389T>C|p.?|187/3696|80/2100||-389|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+389T>C|p.?|193/7151|80/5655||-389|	GT:AD:DP:GQ	0/1:15,17:32:48
-17	41276247	.	A	G	.	.	gnomad_exomes_an=31318;gnomad_exomes_hom=1611;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125468.4;clinvar_germline_classification=Benign;ANN=G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-19-115T>C|p.?|95/7088|-19/5592||115|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-115T>C|p.?|89/7028|-106/5451||115|,G|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||115|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-115T>C|p.?|89/3696|-19/2100||115|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-115T>C|p.?|95/7151|-19/5655||115|	GT:AD:DP:GQ	0/1:18,10:28:44
-17	41276348	.	T	C	.	.	clinvar_vcv=VCV000209574.3;clinvar_germline_classification=Benign;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-19-216A>G|p.?|95/7088|-19/5592||216|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-216A>G|p.?|89/7028|-106/5451||216|,C|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||216|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-216A>G|p.?|89/3696|-19/2100||216|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-216A>G|p.?|95/7151|-19/5655||216|	GT:AD:DP:GQ	0/1:17,13:30:47
-17	41277187	.	G	C	.	.	gnomad_exomes_an=29432;gnomad_exomes_hom=4088;gnomad_exomes_het=6345;gnomad_genomes_an=128296;gnomad_genomes_hom=11705;gnomad_genomes_het=29182;clinvar_vcv=VCV000189123.4;clinvar_germline_classification=Benign;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-20+101C>G|p.?|94/7088|-20/5592||-101|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-107+107C>G|p.?|88/7028|-107/5451||-107|,C|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||1055|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-20+107C>G|p.?|88/3696|-20/2100||-107|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-20+101C>G|p.?|94/7151|-20/5655||-101|	GT:AD:DP:GQ	0/1:14,14:28:48
+17	41244000	.	T	C	.	.	gnomad_exomes_an=31346;gnomad_exomes_hom=1591;gnomad_exomes_het=6707;gnomad_genomes_an=250954;gnomad_genomes_hom=16402;gnomad_genomes_het=55703;clinvar_vcv=VCV000041818.87;clinvar_germline_classification=Benign;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.3548A>G|p.Lys1183Arg|3661/7088|3548/5592|1183/1864|0|-1|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.3407A>G|p.Lys1136Arg|3601/7028|3407/5451|1136/1817|0|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.788-951A>G|p.?|807/3682|788/2280||951|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-951A>G|p.?|895/3696|788/2100||951|-1|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3548A>G|p.Lys1183Arg|3661/7151|3548/5655|1183/1885|0|-1|	GT:AD:DP:GQ	0/1:8,18:26:43
+17	41244435	.	T	C	.	.	gnomad_exomes_an=31332;gnomad_exomes_hom=1505;gnomad_exomes_het=6415;gnomad_genomes_an=251032;gnomad_genomes_hom=16145;gnomad_genomes_het=55137;clinvar_vcv=VCV000041815.87;clinvar_germline_classification=Benign;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.3113A>G|p.Glu1038Gly|3226/7088|3113/5592|1038/1864|0|-1|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2972A>G|p.Glu991Gly|3166/7028|2972/5451|991/1817|0|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.788-1386A>G|p.?|807/3682|788/2280||1386|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-1386A>G|p.?|895/3696|788/2100||1386|-1|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3113A>G|p.Glu1038Gly|3226/7151|3113/5655|1038/1885|0|-1|	GT:AD:DP:GQ	0/1:12,14:26:47
+17	41244936	.	G	A	.	.	gnomad_exomes_an=31324;gnomad_exomes_hom=4287;gnomad_exomes_het=6594;gnomad_genomes_an=251034;gnomad_genomes_hom=22738;gnomad_genomes_het=55898;clinvar_vcv=VCV000041812.88;clinvar_germline_classification=Benign;ANN=A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2612C>T|p.Pro871Leu|2725/7088|2612/5592|871/1864|0|-1|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2471C>T|p.Pro824Leu|2665/7028|2471/5451|824/1817|0|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1825C>T|p.?|806/3682|787/2280||-1825|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1825C>T|p.?|894/3696|787/2100||-1825|-1|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2612C>T|p.Pro871Leu|2725/7151|2612/5655|871/1885|0|-1|	GT:AD:DP:GQ	0/1:17,13:30:47
+17	41245237	.	A	G	.	.	gnomad_exomes_an=31314;gnomad_exomes_hom=1492;gnomad_exomes_het=6416;gnomad_genomes_an=250946;gnomad_genomes_hom=16057;gnomad_genomes_het=55063;clinvar_vcv=VCV000125554.83;clinvar_germline_classification=Benign;ANN=G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2311T>C|p.Leu771=|2424/7088|2311/5592|771/1864|0|-1|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2170T>C|p.Leu724=|2364/7028|2170/5451|724/1817|0|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1524T>C|p.?|806/3682|787/2280||-1524|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1524T>C|p.?|894/3696|787/2100||-1524|-1|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2311T>C|p.Leu771=|2424/7151|2311/5655|771/1885|0|-1|	GT:AD:DP:GQ	0/1:18,11:29:46
+17	41245466	.	G	A	.	.	gnomad_exomes_an=31338;gnomad_exomes_hom=1602;gnomad_exomes_het=6709;gnomad_genomes_an=251110;gnomad_genomes_hom=16420;gnomad_genomes_het=55707;clinvar_vcv=VCV000125536.84;clinvar_germline_classification=Benign;ANN=A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|10/23|c.2082C>T|p.Ser694=|2195/7088|2082/5592|694/1864|0|-1|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.1941C>T|p.Ser647=|2135/7028|1941/5451|647/1817|0|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|9/21|c.787+1295C>T|p.?|806/3682|787/2280||-1295|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1295C>T|p.?|894/3696|787/2100||-1295|-1|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2082C>T|p.Ser694=|2195/7151|2082/5655|694/1885|0|-1|	GT:AD:DP:GQ	0/1:11,8:19:48
+17	41247122	.	A	ACCT	.	.	clinvar_vcv=VCV000127125.5;clinvar_germline_classification=Benign;ANN=ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|9/22|c.671-246_671-245insAGG|p.?|784/7088|671/5592||246|-1|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.530-246_530-245insAGG|p.?|724/7028|530/5451||246|-1|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|8/21|c.671-246_671-245insAGG|p.?|690/3682|671/2280||246|-1|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.671-246_671-245insAGG|p.?|778/3696|671/2100||246|-1|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.671-246_671-245insAGG|p.?|784/7151|671/5655||246|-1|	GT:AD:DP:GQ	0/1:18,11:29:45
+17	41247604	.	A	C	.	.	clinvar_vcv=VCV000209447.5;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|9/22|c.670+259T>G|p.?|783/7088|670/5592||-259|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.529+259T>G|p.?|723/7028|529/5451||-259|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|8/21|c.670+259T>G|p.?|689/3682|670/2280||-259|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.670+259T>G|p.?|777/3696|670/2100||-259|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.670+259T>G|p.?|783/7151|670/5655||-259|-1|	GT:AD:DP:GQ	0/1:12,11:23:47
+17	41248164	.	C	T	.	.	clinvar_vcv=VCV000209449.4;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-225G>A|p.?|707/7088|594/5592||225|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-225G>A|p.?|647/7028|453/5451||225|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-225G>A|p.?|613/3682|594/2280||225|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-225G>A|p.?|701/3696|594/2100||225|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-225G>A|p.?|707/7151|594/5655||225|-1|	GT:AD:DP:GQ	0/1:14,7:21:44
+17	41248393	.	C	CAAAAAAAAAA	.	.	ANN=CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-455_594-454insTTTTTTTTTT|p.?|707/7088|594/5592||455|-1|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-455_453-454insTTTTTTTTTT|p.?|647/7028|453/5451||455|-1|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-455_594-454insTTTTTTTTTT|p.?|613/3682|594/2280||455|-1|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-455_594-454insTTTTTTTTTT|p.?|701/3696|594/2100||455|-1|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-455_594-454insTTTTTTTTTT|p.?|707/7151|594/5655||455|-1|	GT:AD:DP:GQ	0/1:9,7:16:48
+17	41248484	.	G	C	.	.	clinvar_vcv=VCV000209450.4;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-545C>G|p.?|707/7088|594/5592||545|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-545C>G|p.?|647/7028|453/5451||545|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-545C>G|p.?|613/3682|594/2280||545|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-545C>G|p.?|701/3696|594/2100||545|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-545C>G|p.?|707/7151|594/5655||545|-1|	GT:AD:DP:GQ	0/1:11,9:20:48
+17	41248588	.	CA	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.594-650del|p.?|707/7088|594/5592||650|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-650del|p.?|647/7028|453/5451||650|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.594-650del|p.?|613/3682|594/2280||650|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-650del|p.?|701/3696|594/2100||650|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-650del|p.?|707/7151|594/5655||650|-1|	GT:AD:DP:GQ	0/1:9,10:19:42
+17	41249094	.	A	G	.	.	gnomad_exomes_an=31332;gnomad_exomes_hom=1602;gnomad_exomes_het=6703;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000209451.5;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/22|c.593+167T>C|p.?|706/7088|593/5592||-167|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.452+167T>C|p.?|646/7028|452/5451||-167|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/21|c.593+167T>C|p.?|612/3682|593/2280||-167|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.593+167T>C|p.?|700/3696|593/2100||-167|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.593+167T>C|p.?|706/7151|593/5655||-167|-1|	GT:AD:DP:GQ	0/1:9,7:16:48
+17	41249363	.	TA	T	.	.	gnomad_exomes_an=31286;gnomad_exomes_hom=1497;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.548-58del|p.?|661/7088|548/5592||58|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-58del|p.?|601/7028|407/5451||58|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.548-58del|p.?|567/3682|548/2280||58|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-58del|p.?|655/3696|548/2100||58|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-58del|p.?|661/7151|548/5655||58|-1|	GT:AD:DP:GQ	0/1:12,13:25:48
+17	41250047	.	C	CT	.	.	ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.548-742_548-741insA|p.?|661/7088|548/5592||742|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-742_407-741insA|p.?|601/7028|407/5451||742|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.548-742_548-741insA|p.?|567/3682|548/2280||742|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-742_548-741insA|p.?|655/3696|548/2100||742|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-742_548-741insA|p.?|661/7151|548/5655||742|-1|	GT:AD:DP:GQ	0/1:13,7:20:18
+17	41250678	.	C	CT	.	.	clinvar_vcv=VCV000209458.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+1113_547+1114insA|p.?|660/7088|547/5592||-1114|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+1113_406+1114insA|p.?|600/7028|406/5451||-1114|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+1113_547+1114insA|p.?|566/3682|547/2280||-1114|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+1113_547+1114insA|p.?|654/3696|547/2100||-1114|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+1113_547+1114insA|p.?|660/7151|547/5655||-1114|-1|	GT:AD:DP:GQ	0/1:6,16:22:42
+17	41250923	.	T	C	.	.	clinvar_vcv=VCV000209460.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+869A>G|p.?|660/7088|547/5592||-869|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+869A>G|p.?|600/7028|406/5451||-869|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+869A>G|p.?|566/3682|547/2280||-869|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+869A>G|p.?|654/3696|547/2100||-869|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+869A>G|p.?|660/7151|547/5655||-869|-1|	GT:AD:DP:GQ	0/1:13,9:22:47
+17	41251495	.	C	G	.	.	clinvar_vcv=VCV000209463.4;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+297G>C|p.?|660/7088|547/5592||-297|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+297G>C|p.?|600/7028|406/5451||-297|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+297G>C|p.?|566/3682|547/2280||-297|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+297G>C|p.?|654/3696|547/2100||-297|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+297G>C|p.?|660/7151|547/5655||-297|-1|	GT:AD:DP:GQ	0/1:11,15:26:48
+17	41251646	.	T	A	.	.	gnomad_exomes_an=31294;gnomad_exomes_hom=1592;gnomad_exomes_het=6693;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125879.7;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|7/22|c.547+146A>T|p.?|660/7088|547/5592||-146|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+146A>T|p.?|600/7028|406/5451||-146|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|6/21|c.547+146A>T|p.?|566/3682|547/2280||-146|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+146A>T|p.?|654/3696|547/2100||-146|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+146A>T|p.?|660/7151|547/5655||-146|-1|	GT:AD:DP:GQ	0/1:11,8:19:48
+17	41252575	.	G	A	.	.	clinvar_vcv=VCV000209466.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-678C>T|p.?|555/7088|442/5592||678|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-678C>T|p.?|495/7028|301/5451||678|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-678C>T|p.?|461/3682|442/2280||678|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-678C>T|p.?|549/3696|442/2100||678|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-678C>T|p.?|555/7151|442/5655||678|-1|	GT:AD:DP:GQ:PS	1|1:0,3:3:5:41252575
+17	41252591	.	C	CAT	.	.	clinvar_vcv=VCV000264796.2;clinvar_germline_classification=Benign;ANN=CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-695_442-694insAT|p.?|555/7088|442/5592||695|-1|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-695_301-694insAT|p.?|495/7028|301/5451||695|-1|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-695_442-694insAT|p.?|461/3682|442/2280||695|-1|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-695_442-694insAT|p.?|549/3696|442/2100||695|-1|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-695_442-694insAT|p.?|555/7151|442/5655||695|-1|	GT:AD:DP:GQ:PS	1|1:0,2:2:4:41252575
+17	41254174	.	A	G	.	.	clinvar_vcv=VCV000209478.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1965T>C|p.?|554/7088|441/5592||-1965|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1965T>C|p.?|494/7028|300/5451||-1965|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1965T>C|p.?|460/3682|441/2280||-1965|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1965T>C|p.?|548/3696|441/2100||-1965|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1965T>C|p.?|554/7151|441/5655||-1965|-1|	GT:AD:DP:GQ	0/1:14,13:27:48
+17	41254374	.	C	CTTTTTTTT	.	.	ANN=CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1764_441+1765insAAAAAAAA|p.?|554/7088|441/5592||-1765|-1|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1764_300+1765insAAAAAAAA|p.?|494/7028|300/5451||-1765|-1|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1764_441+1765insAAAAAAAA|p.?|460/3682|441/2280||-1765|-1|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1764_441+1765insAAAAAAAA|p.?|548/3696|441/2100||-1765|-1|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1764_441+1765insAAAAAAAA|p.?|554/7151|441/5655||-1765|-1|	GT:AD:DP:GQ	0/1:6,7:13:48
+17	41254405	.	C	T	.	.	clinvar_vcv=VCV000264778.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1734G>A|p.?|554/7088|441/5592||-1734|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1734G>A|p.?|494/7028|300/5451||-1734|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1734G>A|p.?|460/3682|441/2280||-1734|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1734G>A|p.?|548/3696|441/2100||-1734|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1734G>A|p.?|554/7151|441/5655||-1734|-1|	GT:AD:DP:GQ	0/1:5,9:14:43
+17	41254486	.	T	G	.	.	clinvar_vcv=VCV000209479.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1653A>C|p.?|554/7088|441/5592||-1653|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1653A>C|p.?|494/7028|300/5451||-1653|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1653A>C|p.?|460/3682|441/2280||-1653|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1653A>C|p.?|548/3696|441/2100||-1653|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1653A>C|p.?|554/7151|441/5655||-1653|-1|	GT:AD:DP:GQ	0/1:8,15:23:46
+17	41254965	.	C	CT	.	.	clinvar_vcv=VCV000264845.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1173_441+1174insA|p.?|554/7088|441/5592||-1174|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1173_300+1174insA|p.?|494/7028|300/5451||-1174|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1173_441+1174insA|p.?|460/3682|441/2280||-1174|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1173_441+1174insA|p.?|548/3696|441/2100||-1174|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1173_441+1174insA|p.?|554/7151|441/5655||-1174|-1|	GT:AD:DP:GQ	0/1:14,8:22:22
+17	41255102	.	A	G	.	.	clinvar_vcv=VCV000209483.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1037T>C|p.?|554/7088|441/5592||-1037|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1037T>C|p.?|494/7028|300/5451||-1037|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1037T>C|p.?|460/3682|441/2280||-1037|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1037T>C|p.?|548/3696|441/2100||-1037|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1037T>C|p.?|554/7151|441/5655||-1037|-1|	GT:AD:DP:GQ:PS	0|1:19,12:31:46:41255102
+17	41255111	.	A	T	.	.	clinvar_vcv=VCV000209484.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1028T>A|p.?|554/7088|441/5592||-1028|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1028T>A|p.?|494/7028|300/5451||-1028|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1028T>A|p.?|460/3682|441/2280||-1028|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1028T>A|p.?|548/3696|441/2100||-1028|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1028T>A|p.?|554/7151|441/5655||-1028|-1|	GT:AD:DP:GQ:PS	0|1:19,12:31:46:41255102
+17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64del|p.?|554/7088|441/5592||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64del|p.?|494/7028|300/5451||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64del|p.?|460/3682|441/2280||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64del|p.?|548/3696|441/2100||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64del|p.?|554/7151|441/5655||-64|-1|	GT:AD:DP:GQ:PS	0|1:11,6:17:43:41256074
+17	41256089	.	AAAAAAAAAGAAAAG	A	.	.	gnomad_exomes_an=28388;gnomad_exomes_hom=1079;gnomad_exomes_het=5744;gnomad_genomes_an=167932;gnomad_genomes_hom=9911;gnomad_genomes_het=23697;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+36_441+49del|p.?|554/7088|441/5592||-36|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+36_300+49del|p.?|494/7028|300/5451||-36|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+36_441+49del|p.?|460/3682|441/2280||-36|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+36_441+49del|p.?|548/3696|441/2100||-36|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+36_441+49del|p.?|554/7151|441/5655||-36|-1|	GT:AD:DP:GQ:PS	0|1:13,6:19:43:41256074
+17	41257134	.	T	C	.	.	gnomad_exomes_an=31346;gnomad_exomes_hom=4418;gnomad_exomes_het=6505;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125614.7;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.213-161A>G|p.?|326/7088|213/5592||161|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-161A>G|p.?|266/7028|72/5451||161|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.213-161A>G|p.?|232/3682|213/2280||161|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-161A>G|p.?|320/3696|213/2100||161|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-161A>G|p.?|326/7151|213/5655||161|-1|	GT:AD:DP:GQ	0/1:14,15:29:48
+17	41257458	.	A	C	.	.	clinvar_vcv=VCV000209489.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.213-485T>G|p.?|326/7088|213/5592||485|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-485T>G|p.?|266/7028|72/5451||485|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.213-485T>G|p.?|232/3682|213/2280||485|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-485T>G|p.?|320/3696|213/2100||485|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-485T>G|p.?|326/7151|213/5655||485|-1|	GT:AD:DP:GQ	0/1:11,15:26:48
+17	41258043	.	C	T	.	.	clinvar_vcv=VCV000209491.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.212+430G>A|p.?|325/7088|212/5592||-430|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+430G>A|p.?|265/7028|71/5451||-430|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.212+430G>A|p.?|231/3682|212/2280||-430|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+430G>A|p.?|319/3696|212/2100||-430|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+430G>A|p.?|325/7151|212/5655||-430|-1|	GT:AD:DP:GQ	0/1:14,13:27:48
+17	41258135	.	T	TA	.	.	ANN=TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|4/22|c.212+337_212+338insT|p.?|325/7088|212/5592||-338|-1|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+337_71+338insT|p.?|265/7028|71/5451||-338|-1|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|3/21|c.212+337_212+338insT|p.?|231/3682|212/2280||-338|-1|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+337_212+338insT|p.?|319/3696|212/2100||-338|-1|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+337_212+338insT|p.?|325/7151|212/5655||-338|-1|	GT:AD:DP:GQ	1/1:3,11:14:4
+17	41259049	.	C	T	.	.	clinvar_vcv=VCV000209494.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-499G>A|p.?|248/7088|135/5592||499|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-499G>A|p.?|188/7028|-7/5451||499|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-499G>A|p.?|154/3682|135/2280||499|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-499G>A|p.?|242/3696|135/2100||499|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-499G>A|p.?|248/7151|135/5655||499|-1|	GT:AD:DP:GQ	0/1:8,8:16:48
+17	41259079	.	A	ATT	.	.	ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-530_135-529insAA|p.?|248/7088|135/5592||530|-1|,ATT|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-530_-7-529insAA|p.?|188/7028|-7/5451||530|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-530_135-529insAA|p.?|154/3682|135/2280||530|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-530_135-529insAA|p.?|242/3696|135/2100||530|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-530_135-529insAA|p.?|248/7151|135/5655||530|-1|	GT:AD:DP:GQ	0/1:10,3:13:7
+17	41259113	.	G	A	.	.	clinvar_vcv=VCV000264811.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-563C>T|p.?|248/7088|135/5592||563|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-563C>T|p.?|188/7028|-7/5451||563|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-563C>T|p.?|154/3682|135/2280||563|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-563C>T|p.?|242/3696|135/2100||563|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-563C>T|p.?|248/7151|135/5655||563|-1|	GT:AD:DP:GQ	0/1:11,8:19:48
+17	41260352	.	C	CA	.	.	clinvar_vcv=VCV000264791.2;clinvar_germline_classification=Benign;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-1803_135-1802insT|p.?|248/7088|135/5592||1803|-1|,CA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-1803_-7-1802insT|p.?|188/7028|-7/5451||1803|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-1803_135-1802insT|p.?|154/3682|135/2280||1803|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-1803_135-1802insT|p.?|242/3696|135/2100||1803|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-1803_135-1802insT|p.?|248/7151|135/5655||1803|-1|	GT:AD:DP:GQ	0/1:11,8:19:43
+17	41260723	.	C	CAAAAA	.	.	ANN=CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2174_135-2173insTTTTT|p.?|248/7088|135/5592||2174|-1|,CAAAAA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2174_-7-2173insTTTTT|p.?|188/7028|-7/5451||2174|-1|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2174_135-2173insTTTTT|p.?|154/3682|135/2280||2174|-1|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2174_135-2173insTTTTT|p.?|242/3696|135/2100||2174|-1|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2174_135-2173insTTTTT|p.?|248/7151|135/5655||2174|-1|	GT:AD:DP:GQ	0/1:1,1:2:20
+17	41260808	.	A	G	.	.	clinvar_vcv=VCV000209499.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2258T>C|p.?|248/7088|135/5592||2258|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2258T>C|p.?|188/7028|-7/5451||2258|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2258T>C|p.?|154/3682|135/2280||2258|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2258T>C|p.?|242/3696|135/2100||2258|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2258T>C|p.?|248/7151|135/5655||2258|-1|	GT:AD:DP:GQ	0/1:12,3:15:32
+17	41261058	.	T	TCTATCTATCTACCTAC	.	.	clinvar_vcv=VCV000264813.2;clinvar_germline_classification=Benign;ANN=TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7088|135/5592||2509|-1|,TCTATCTATCTACCTAC|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2509_-7-2508insGTAGGTAGATAGATAG|p.?|188/7028|-7/5451||2509|-1|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|154/3682|135/2280||2509|-1|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|242/3696|135/2100||2509|-1|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7151|135/5655||2509|-1|	GT:AD:DP:GQ	0/1:9,11:20:48
+17	41261233	.	C	T	.	.	clinvar_vcv=VCV000209503.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-2683G>A|p.?|248/7088|135/5592||2683|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2683G>A|p.?|188/7028|-7/5451||2683|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-2683G>A|p.?|154/3682|135/2280||2683|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2683G>A|p.?|242/3696|135/2100||2683|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2683G>A|p.?|248/7151|135/5655||2683|-1|	GT:AD:DP:GQ	0/1:12,15:27:48
+17	41263044	.	A	G	.	.	clinvar_vcv=VCV000209512.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-4494T>C|p.?|248/7088|135/5592||4494|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4494T>C|p.?|188/7028|-7/5451||4494|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-4494T>C|p.?|154/3682|135/2280||4494|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4494T>C|p.?|242/3696|135/2100||4494|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4494T>C|p.?|248/7151|135/5655||4494|-1|	GT:AD:DP:GQ	0/1:7,7:14:48
+17	41263117	.	C	CA	.	.	ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.135-4568_135-4567insT|p.?|248/7088|135/5592||4568|-1|,CA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4568_-7-4567insT|p.?|188/7028|-7/5451||4568|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.135-4568_135-4567insT|p.?|154/3682|135/2280||4568|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4568_135-4567insT|p.?|242/3696|135/2100||4568|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4568_135-4567insT|p.?|248/7151|135/5655||4568|-1|	GT:AD:DP:GQ	0/1:13,10:23:34
+17	41263566	.	T	C	.	.	clinvar_vcv=VCV000209516.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+4177A>G|p.?|247/7088|134/5592||-4177|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5016A>G|p.?|188/7028|-7/5451||5016|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+4177A>G|p.?|153/3682|134/2280||-4177|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+4177A>G|p.?|241/3696|134/2100||-4177|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+4177A>G|p.?|247/7151|134/5655||-4177|-1|	GT:AD:DP:GQ	0/1:11,8:19:48
+17	41264146	.	G	A	.	.	clinvar_vcv=VCV000209519.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3597C>T|p.?|247/7088|134/5592||-3597|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5596C>T|p.?|188/7028|-7/5451||5596|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3597C>T|p.?|153/3682|134/2280||-3597|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3597C>T|p.?|241/3696|134/2100||-3597|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3597C>T|p.?|247/7151|134/5655||-3597|-1|	GT:AD:DP:GQ	0/1:13,7:20:45
+17	41264364	.	A	G	.	.	clinvar_vcv=VCV000209521.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3379T>C|p.?|247/7088|134/5592||-3379|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5814T>C|p.?|188/7028|-7/5451||5814|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3379T>C|p.?|153/3682|134/2280||-3379|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3379T>C|p.?|241/3696|134/2100||-3379|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3379T>C|p.?|247/7151|134/5655||-3379|-1|	GT:AD:DP:GQ	0/1:8,16:24:45
+17	41264739	.	C	T	.	.	clinvar_vcv=VCV000264785.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3004G>A|p.?|247/7088|134/5592||-3004|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6189G>A|p.?|188/7028|-7/5451||6189|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3004G>A|p.?|153/3682|134/2280||-3004|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3004G>A|p.?|241/3696|134/2100||-3004|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3004G>A|p.?|247/7151|134/5655||-3004|-1|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
+17	41264740	.	TGA	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+3001_134+3002del|p.?|247/7088|134/5592||-3001|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6192_-7-6191del|p.?|188/7028|-7/5451||6191|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+3001_134+3002del|p.?|153/3682|134/2280||-3001|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3001_134+3002del|p.?|241/3696|134/2100||-3001|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3001_134+3002del|p.?|247/7151|134/5655||-3001|-1|	GT:AD:DP:GQ	0/1:14,16:30:48
+17	41264743	.	CT	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2999del|p.?|247/7088|134/5592||-2999|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6194del|p.?|188/7028|-7/5451||6194|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2999del|p.?|153/3682|134/2280||-2999|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2999del|p.?|241/3696|134/2100||-2999|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2999del|p.?|247/7151|134/5655||-2999|-1|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
+17	41264749	.	C	G	.	.	clinvar_vcv=VCV000264823.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2994G>C|p.?|247/7088|134/5592||-2994|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6199G>C|p.?|188/7028|-7/5451||6199|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2994G>C|p.?|153/3682|134/2280||-2994|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2994G>C|p.?|241/3696|134/2100||-2994|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2994G>C|p.?|247/7151|134/5655||-2994|-1|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
+17	41264750	.	A	T	.	.	clinvar_vcv=VCV000264824.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2993T>A|p.?|247/7088|134/5592||-2993|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6200T>A|p.?|188/7028|-7/5451||6200|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2993T>A|p.?|153/3682|134/2280||-2993|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2993T>A|p.?|241/3696|134/2100||-2993|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2993T>A|p.?|247/7151|134/5655||-2993|-1|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
+17	41264751	.	A	AGGG	.	.	ANN=AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2991_134+2992insCCC|p.?|247/7088|134/5592||-2992|-1|,AGGG|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6202_-7-6201insCCC|p.?|188/7028|-7/5451||6202|-1|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2991_134+2992insCCC|p.?|153/3682|134/2280||-2992|-1|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2991_134+2992insCCC|p.?|241/3696|134/2100||-2992|-1|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2991_134+2992insCCC|p.?|247/7151|134/5655||-2992|-1|	GT:AD:DP:GQ:PS	0|1:14,15:29:48:41264739
+17	41264753	.	C	T	.	.	clinvar_vcv=VCV000264819.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2990G>A|p.?|247/7088|134/5592||-2990|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6203G>A|p.?|188/7028|-7/5451||6203|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2990G>A|p.?|153/3682|134/2280||-2990|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2990G>A|p.?|241/3696|134/2100||-2990|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2990G>A|p.?|247/7151|134/5655||-2990|-1|	GT:AD:DP:GQ:PS	0|1:14,13:27:48:41264739
+17	41264755	.	TGAAAC	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+2983_134+2987del|p.?|247/7088|134/5592||-2983|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6210_-7-6206del|p.?|188/7028|-7/5451||6206|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+2983_134+2987del|p.?|153/3682|134/2280||-2983|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2983_134+2987del|p.?|241/3696|134/2100||-2983|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2983_134+2987del|p.?|247/7151|134/5655||-2983|-1|	GT:AD:DP:GQ:PS	0|1:14,13:27:48:41264739
+17	41265776	.	A	G	.	.	clinvar_vcv=VCV000209524.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+1967T>C|p.?|247/7088|134/5592||-1967|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7226T>C|p.?|188/7028|-7/5451||7226|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+1967T>C|p.?|153/3682|134/2280||-1967|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1967T>C|p.?|241/3696|134/2100||-1967|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1967T>C|p.?|247/7151|134/5655||-1967|-1|	GT:AD:DP:GQ	0/1:23,14:37:44
+17	41266407	.	C	CT	.	.	clinvar_vcv=VCV000264777.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+1335_134+1336insA|p.?|247/7088|134/5592||-1336|-1|,CT|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7858_-7-7857insA|p.?|188/7028|-7/5451||7858|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+1335_134+1336insA|p.?|153/3682|134/2280||-1336|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1335_134+1336insA|p.?|241/3696|134/2100||-1336|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1335_134+1336insA|p.?|247/7151|134/5655||-1336|-1|	GT:AD:DP:GQ	0/1:10,8:18:33
+17	41267050	.	G	A	.	.	clinvar_vcv=VCV000209531.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+693C>T|p.?|247/7088|134/5592||-693|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-8500C>T|p.?|188/7028|-7/5451||8500|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+693C>T|p.?|153/3682|134/2280||-693|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+693C>T|p.?|241/3696|134/2100||-693|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+693C>T|p.?|247/7151|134/5655||-693|-1|	GT:AD:DP:GQ	0/1:7,16:23:44
+17	41267518	.	CA	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|3/22|c.134+224del|p.?|247/7088|134/5592||-224|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+8515del|p.?|187/7028|-8/5451||-8515|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|2/21|c.134+224del|p.?|153/3682|134/2280||-224|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+224del|p.?|241/3696|134/2100||-224|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+224del|p.?|247/7151|134/5655||-224|-1|	GT:AD:DP:GQ	0/1:11,8:19:35
+17	41268206	.	A	C	.	.	clinvar_vcv=VCV000209537.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-410T>G|p.?|194/7088|81/5592||410|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7828T>G|p.?|187/7028|-8/5451||-7828|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-410T>G|p.?|100/3682|81/2280||410|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-410T>G|p.?|188/3696|81/2100||410|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-410T>G|p.?|194/7151|81/5655||410|-1|	GT:AD:DP:GQ:PS	0|1:13,9:22:46:41268206
+17	41268208	.	C	CT	.	.	clinvar_vcv=VCV000264808.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-413_81-412insA|p.?|194/7088|81/5592||413|-1|,CT|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7825_-8+7826insA|p.?|187/7028|-8/5451||-7826|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-413_81-412insA|p.?|100/3682|81/2280||413|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-413_81-412insA|p.?|188/3696|81/2100||413|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-413_81-412insA|p.?|194/7151|81/5655||413|-1|	GT:AD:DP:GQ:PS	0|1:13,9:22:46:41268206
+17	41270229	.	T	G	.	.	clinvar_vcv=VCV000209545.2;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2433A>C|p.?|194/7088|81/5592||2433|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5805A>C|p.?|187/7028|-8/5451||-5805|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2433A>C|p.?|100/3682|81/2280||2433|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2433A>C|p.?|188/3696|81/2100||2433|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2433A>C|p.?|194/7151|81/5655||2433|-1|	GT:AD:DP:GQ	0/1:7,17:24:40
+17	41270277	.	C	T	.	.	clinvar_vcv=VCV000209547.2;clinvar_germline_classification=Benign;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2481G>A|p.?|194/7088|81/5592||2481|-1|,T|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5757G>A|p.?|187/7028|-8/5451||-5757|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2481G>A|p.?|100/3682|81/2280||2481|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2481G>A|p.?|188/3696|81/2100||2481|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2481G>A|p.?|194/7151|81/5655||2481|-1|	GT:AD:DP:GQ	0/1:9,13:22:48
+17	41270463	.	G	A	.	.	clinvar_vcv=VCV000209551.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2667C>T|p.?|194/7088|81/5592||2667|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5571C>T|p.?|187/7028|-8/5451||-5571|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2667C>T|p.?|100/3682|81/2280||2667|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2667C>T|p.?|188/3696|81/2100||2667|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2667C>T|p.?|194/7151|81/5655||2667|-1|	GT:AD:DP:GQ	0/1:15,13:28:48
+17	41270666	.	C	A	.	.	clinvar_vcv=VCV000209552.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2870G>T|p.?|194/7088|81/5592||2870|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5368G>T|p.?|187/7028|-8/5451||-5368|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2870G>T|p.?|100/3682|81/2280||2870|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2870G>T|p.?|188/3696|81/2100||2870|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2870G>T|p.?|194/7151|81/5655||2870|-1|	GT:AD:DP:GQ	0/1:11,4:15:43
+17	41270778	.	C	CT	.	.	clinvar_vcv=VCV000264797.2;clinvar_germline_classification=Benign;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-2983_81-2982insA|p.?|194/7088|81/5592||2983|-1|,CT|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5255_-8+5256insA|p.?|187/7028|-8/5451||-5256|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-2983_81-2982insA|p.?|100/3682|81/2280||2983|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2983_81-2982insA|p.?|188/3696|81/2100||2983|-1|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2983_81-2982insA|p.?|194/7151|81/5655||2983|-1|	GT:AD:DP:GQ	0/1:11,5:16:14
+17	41271293	.	GA	G	.	.	ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.81-3498del|p.?|194/7088|81/5592||3498|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+4740del|p.?|187/7028|-8/5451||-4740|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.81-3498del|p.?|100/3682|81/2280||3498|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-3498del|p.?|188/3696|81/2100||3498|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-3498del|p.?|194/7151|81/5655||3498|-1|	GT:AD:DP:GQ	0/1:10,10:20:48
+17	41273095	.	G	A	.	.	clinvar_vcv=VCV000209559.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2939C>T|p.?|193/7088|80/5592||-2939|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2939C>T|p.?|187/7028|-8/5451||-2939|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2939C>T|p.?|99/3682|80/2280||-2939|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2939C>T|p.?|187/3696|80/2100||-2939|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2939C>T|p.?|193/7151|80/5655||-2939|-1|	GT:AD:DP:GQ	0/1:12,8:20:47
+17	41273348	.	T	C	.	.	clinvar_vcv=VCV000209561.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2686A>G|p.?|193/7088|80/5592||-2686|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2686A>G|p.?|187/7028|-8/5451||-2686|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2686A>G|p.?|99/3682|80/2280||-2686|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2686A>G|p.?|187/3696|80/2100||-2686|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2686A>G|p.?|193/7151|80/5655||-2686|-1|	GT:AD:DP:GQ	0/1:18,13:31:47
+17	41273379	.	G	C	.	.	clinvar_vcv=VCV000209562.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2655C>G|p.?|193/7088|80/5592||-2655|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2655C>G|p.?|187/7028|-8/5451||-2655|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2655C>G|p.?|99/3682|80/2280||-2655|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2655C>G|p.?|187/3696|80/2100||-2655|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2655C>G|p.?|193/7151|80/5655||-2655|-1|	GT:AD:DP:GQ	0/1:19,14:33:47
+17	41273537	.	A	C	.	.	clinvar_vcv=VCV000209564.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2497T>G|p.?|193/7088|80/5592||-2497|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2497T>G|p.?|187/7028|-8/5451||-2497|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2497T>G|p.?|99/3682|80/2280||-2497|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2497T>G|p.?|187/3696|80/2100||-2497|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2497T>G|p.?|193/7151|80/5655||-2497|-1|	GT:AD:DP:GQ	0/1:14,19:33:48
+17	41274778	.	G	A	.	.	clinvar_vcv=VCV000209565.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+1256C>T|p.?|193/7088|80/5592||-1256|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1256C>T|p.?|187/7028|-8/5451||-1256|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+1256C>T|p.?|99/3682|80/2280||-1256|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1256C>T|p.?|187/3696|80/2100||-1256|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1256C>T|p.?|193/7151|80/5655||-1256|-1|	GT:AD:DP:GQ	0/1:11,16:27:48
+17	41274906	.	G	A	.	.	clinvar_vcv=VCV000209568.2;clinvar_germline_classification=Benign;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+1128C>T|p.?|193/7088|80/5592||-1128|-1|,A|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1128C>T|p.?|187/7028|-8/5451||-1128|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+1128C>T|p.?|99/3682|80/2280||-1128|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1128C>T|p.?|187/3696|80/2100||-1128|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1128C>T|p.?|193/7151|80/5655||-1128|-1|	GT:AD:DP:GQ	0/1:17,10:27:47
+17	41275081	.	G	GA	.	.	clinvar_vcv=VCV000209569.2;clinvar_germline_classification=Benign;ANN=GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+952_80+953insT|p.?|193/7088|80/5592||-953|-1|,GA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+952_-8+953insT|p.?|187/7028|-8/5451||-953|-1|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+952_80+953insT|p.?|99/3682|80/2280||-953|-1|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+952_80+953insT|p.?|187/3696|80/2100||-953|-1|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+952_80+953insT|p.?|193/7151|80/5655||-953|-1|	GT:AD:DP:GQ	0/1:10,12:22:47
+17	41275151	.	G	C	.	.	clinvar_vcv=VCV000209570.2;clinvar_germline_classification=Benign;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+883C>G|p.?|193/7088|80/5592||-883|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+883C>G|p.?|187/7028|-8/5451||-883|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+883C>G|p.?|99/3682|80/2280||-883|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+883C>G|p.?|187/3696|80/2100||-883|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+883C>G|p.?|193/7151|80/5655||-883|-1|	GT:AD:DP:GQ	0/1:15,13:28:48
+17	41275366	.	GTTTTTTT	G	.	.	ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+661_80+667del|p.?|193/7088|80/5592||-661|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+661_-8+667del|p.?|187/7028|-8/5451||-661|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+661_80+667del|p.?|99/3682|80/2280||-661|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+661_80+667del|p.?|187/3696|80/2100||-661|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+661_80+667del|p.?|193/7151|80/5655||-661|-1|	GT:AD:DP:GQ	0/1:10,11:21:48
+17	41275645	.	A	G	.	.	clinvar_vcv=VCV000209571.3;clinvar_germline_classification=Benign;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+389T>C|p.?|193/7088|80/5592||-389|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+389T>C|p.?|187/7028|-8/5451||-389|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+389T>C|p.?|99/3682|80/2280||-389|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+389T>C|p.?|187/3696|80/2100||-389|-1|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+389T>C|p.?|193/7151|80/5655||-389|-1|	GT:AD:DP:GQ	0/1:15,17:32:48
+17	41276247	.	A	G	.	.	gnomad_exomes_an=31318;gnomad_exomes_hom=1611;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_vcv=VCV000125468.4;clinvar_germline_classification=Benign;ANN=G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-19-115T>C|p.?|95/7088|-19/5592||115|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-115T>C|p.?|89/7028|-106/5451||115|-1|,G|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||115|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-115T>C|p.?|89/3696|-19/2100||115|-1|,G|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-115T>C|p.?|95/7151|-19/5655||115|-1|	GT:AD:DP:GQ	0/1:18,10:28:44
+17	41276348	.	T	C	.	.	clinvar_vcv=VCV000209574.3;clinvar_germline_classification=Benign;ANN=C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-19-216A>G|p.?|95/7088|-19/5592||216|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-216A>G|p.?|89/7028|-106/5451||216|-1|,C|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||216|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-216A>G|p.?|89/3696|-19/2100||216|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-216A>G|p.?|95/7151|-19/5655||216|-1|	GT:AD:DP:GQ	0/1:17,13:30:47
+17	41277187	.	G	C	.	.	gnomad_exomes_an=29432;gnomad_exomes_hom=4088;gnomad_exomes_het=6345;gnomad_genomes_an=128296;gnomad_genomes_hom=11705;gnomad_genomes_het=29182;clinvar_vcv=VCV000189123.4;clinvar_germline_classification=Benign;ANN=C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|1/22|c.-20+101C>G|p.?|94/7088|-20/5592||-101|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-107+107C>G|p.?|88/7028|-107/5451||-107|-1|,C|upstream_gene_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|||||||1055|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-20+107C>G|p.?|88/3696|-20/2100||-107|-1|,C|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-20+101C>G|p.?|94/7151|-20/5655||-101|-1|	GT:AD:DP:GQ	0/1:14,14:28:48
 MT	152	.	T	C	.	.	.	GT:GQ:AD:DP	1/1:98:2,10582:10584
 MT	263	.	A	G	.	.	clinvar_vcv=VCV000441147.1;clinvar_germline_classification=not provided	GT:GQ:AD:DP	1/1:98:0,7628:7628
 MT	302	.	A	AC	.	.	.	GT:GQ:AD:DP	1/1:97:40,3496:3536
diff --git a/src/seqvars/prefilter/mod.rs b/src/seqvars/prefilter/mod.rs
index 1b29059e..0bfa625d 100644
--- a/src/seqvars/prefilter/mod.rs
+++ b/src/seqvars/prefilter/mod.rs
@@ -158,7 +158,6 @@ async fn run_filtration(
         if bytes_read == 0 {
             break; // EOF
         }
-        dbg!(&input_record);
 
         let (frequency, exon_distance) = get_freq_and_distance(&input_record)?;
         if let Some(exon_distance) = exon_distance {
diff --git a/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_arg.snap b/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_arg.snap
index 048a4f6b..a1f85d72 100644
--- a/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_arg.snap
+++ b/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_arg.snap
@@ -14,7 +14,7 @@ expression: "std::fs::read_to_string(format!(\"{}/out-1.vcf\",\n            tmpd
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -56,5 +56,5 @@ expression: "std::fs::read_to_string(format!(\"{}/out-1.vcf\",\n            tmpd
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 ##x-varfish-prefilter-params={"prefilter_path":"<stripped>","max_freq":0.01,"max_exon_dist":200}
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|	GT:AD:DP:GQ	/0/0:29:29:87	/0/1:23:36:99	/0/1:15:32:99
+17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|-1|	GT:AD:DP:GQ	/0/0:29:29:87	/0/1:23:36:99	/0/1:15:32:99
 MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0:2757:99	/1/1:0:2392:99	/1/1:0:1621:99
diff --git a/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_file.snap b/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_file.snap
index 048a4f6b..a1f85d72 100644
--- a/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_file.snap
+++ b/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__single_output_file.snap
@@ -14,7 +14,7 @@ expression: "std::fs::read_to_string(format!(\"{}/out-1.vcf\",\n            tmpd
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -56,5 +56,5 @@ expression: "std::fs::read_to_string(format!(\"{}/out-1.vcf\",\n            tmpd
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 ##x-varfish-prefilter-params={"prefilter_path":"<stripped>","max_freq":0.01,"max_exon_dist":200}
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|	GT:AD:DP:GQ	/0/0:29:29:87	/0/1:23:36:99	/0/1:15:32:99
+17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|-1|	GT:AD:DP:GQ	/0/0:29:29:87	/0/1:23:36:99	/0/1:15:32:99
 MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0:2757:99	/1/1:0:2392:99	/1/1:0:1621:99
diff --git a/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg-2.snap b/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg-2.snap
index 9dcd052f..125a3111 100644
--- a/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg-2.snap
+++ b/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg-2.snap
@@ -14,7 +14,7 @@ expression: "std::fs::read_to_string(format!(\"{}/out-2.vcf\",\n            tmpd
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
diff --git a/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg.snap b/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg.snap
index 048a4f6b..a1f85d72 100644
--- a/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg.snap
+++ b/src/seqvars/prefilter/snapshots/varfish_server_worker__seqvars__prefilter__test__two_output_arg.snap
@@ -14,7 +14,7 @@ expression: "std::fs::read_to_string(format!(\"{}/out-1.vcf\",\n            tmpd
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -56,5 +56,5 @@ expression: "std::fs::read_to_string(format!(\"{}/out-1.vcf\",\n            tmpd
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 ##x-varfish-prefilter-params={"prefilter_path":"<stripped>","max_freq":0.01,"max_exon_dist":200}
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|	GT:AD:DP:GQ	/0/0:29:29:87	/0/1:23:36:99	/0/1:15:32:99
+17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|-1|	GT:AD:DP:GQ	/0/0:29:29:87	/0/1:23:36:99	/0/1:15:32:99
 MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0:2757:99	/1/1:0:2392:99	/1/1:0:1621:99
diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs
index a507a609..2a2266e2 100644
--- a/src/seqvars/query/interpreter/frequency.rs
+++ b/src/seqvars/query/interpreter/frequency.rs
@@ -27,21 +27,21 @@ pub fn passes(query: &CaseQuery, s: &VariantRecord) -> Result<bool, anyhow::Erro
             );
             return Ok(false);
         }
-        if frequency.gnomad_mt.enabled
-            && (frequency.gnomad_mt.frequency.is_some()
-                && s.population_frequencies.gnomad_mt.af()
-                    > frequency.gnomad_mt.frequency.expect("tested before")
-                || frequency.gnomad_mt.heteroplasmic.is_some()
-                    && s.population_frequencies.gnomad_mt.het
-                        > frequency.gnomad_mt.heteroplasmic.expect("tested before")
-                || frequency.gnomad_mt.homoplasmic.is_some()
-                    && s.population_frequencies.gnomad_mt.hom
-                        > frequency.gnomad_mt.homoplasmic.expect("tested before"))
+        if frequency.gnomad_mtdna.enabled
+            && (frequency.gnomad_mtdna.frequency.is_some()
+                && s.population_frequencies.gnomad_mtdna.af()
+                    > frequency.gnomad_mtdna.frequency.expect("tested before")
+                || frequency.gnomad_mtdna.heteroplasmic.is_some()
+                    && s.population_frequencies.gnomad_mtdna.het
+                        > frequency.gnomad_mtdna.heteroplasmic.expect("tested before")
+                || frequency.gnomad_mtdna.homoplasmic.is_some()
+                    && s.population_frequencies.gnomad_mtdna.hom
+                        > frequency.gnomad_mtdna.homoplasmic.expect("tested before"))
         {
             tracing::trace!(
                 "variant {:?} fails gnomAD-MT frequency filter {:?}",
                 s,
-                &frequency.gnomad_mt
+                &frequency.gnomad_mtdna
             );
             return Ok(false);
         }
@@ -108,8 +108,8 @@ mod test {
             VcfVariant,
         },
         query::{
-            CaseQuery, GnomadNuclearFrequencySettings, HelixMtDbFrequencySettings,
-            QuerySettingsFrequency,
+            CaseQuery, GnomadMitochondrialFrequencySettings, GnomadNuclearFrequencySettings,
+            HelixMtDbFrequencySettings, QuerySettingsFrequency,
         },
     };
 
@@ -235,7 +235,13 @@ mod test {
             ..Default::default()
         };
 
-        assert_eq!(super::passes(&query, &seq_var)?, expected_pass_all);
+        assert_eq!(
+            super::passes(&query, &seq_var)?,
+            expected_pass_all,
+            "query: {:#?}, seq_var: {:#?}",
+            query,
+            seq_var
+        );
 
         Ok(())
     }
@@ -362,7 +368,13 @@ mod test {
             ..Default::default()
         };
 
-        assert_eq!(super::passes(&query, &seq_var)?, expected_pass_all);
+        assert_eq!(
+            super::passes(&query, &seq_var)?,
+            expected_pass_all,
+            "query: {:#?}, seq_var: {:#?}",
+            query,
+            seq_var
+        );
 
         Ok(())
     }
@@ -382,9 +394,9 @@ mod test {
     // frequency: pass [hom count]
     #[case(1000, 0, 1, true, Some(0.002), None, None, true)]
     // frequency: fail [hom count]
-    #[case(1000, 0, 2, true, Some(0.002), None, None, false)]
+    #[case(1000, 0, 3, true, Some(0.002), None, None, false)]
     // frequency: pass [hom count] (fail but filter is disabled)
-    #[case(1000, 0, 2, false, Some(0.002), None, None, true)]
+    #[case(1000, 0, 3, false, Some(0.002), None, None, true)]
     // -- heteroplasmy count ------------------------------------------------
     // het. count: pass (no filter value)
     #[case(1000, 1, 0, true, None, None, None, true)]
@@ -466,7 +478,13 @@ mod test {
             ..Default::default()
         };
 
-        assert_eq!(super::passes(&query, &seq_var)?, expected_pass_all);
+        assert_eq!(
+            super::passes(&query, &seq_var)?,
+            expected_pass_all,
+            "query: {:#?}, seq_var: {:#?}",
+            query,
+            seq_var
+        );
 
         Ok(())
     }
@@ -486,9 +504,9 @@ mod test {
     // frequency: pass [hom count]
     #[case(1000, 0, 1, true, Some(0.002), None, None, true)]
     // frequency: fail [hom count]
-    #[case(1000, 0, 2, true, Some(0.002), None, None, false)]
+    #[case(1000, 0, 3, true, Some(0.002), None, None, false)]
     // frequency: pass [hom count] (fail but filter is disabled)
-    #[case(1000, 0, 2, false, Some(0.002), None, None, true)]
+    #[case(1000, 0, 3, false, Some(0.002), None, None, true)]
     // -- heteroplasmy count ------------------------------------------------
     // het. count: pass (no filter value)
     #[case(1000, 1, 0, true, None, None, None, true)]
@@ -509,9 +527,9 @@ mod test {
     #[case(1000, 0, 2, false, None, None, Some(1), true)]
     #[allow(clippy::too_many_arguments)]
     fn passes_frequency_gnomad_mtdna(
-        #[case] seqvar_gnomad_genomes_an: i32,
-        #[case] seqvar_gnomad_genomes_het: i32,
-        #[case] seqvar_gnomad_genomes_hom: i32,
+        #[case] seqvar_gnomad_mtdna_an: i32,
+        #[case] seqvar_gnomad_mtdna_het: i32,
+        #[case] seqvar_gnomad_mtdna_hom: i32,
         #[case] query_gnomad_mtdna_enabled: bool,
         #[case] query_gnomad_mtdna_frequency: Option<f32>,
         #[case] query_gnomad_mtdna_heteroplasmic: Option<i32>,
@@ -520,11 +538,11 @@ mod test {
     ) -> Result<(), anyhow::Error> {
         let query = CaseQuery {
             frequency: QuerySettingsFrequency {
-                gnomad_genomes: GnomadNuclearFrequencySettings {
+                gnomad_mtdna: GnomadMitochondrialFrequencySettings {
                     enabled: query_gnomad_mtdna_enabled,
                     frequency: query_gnomad_mtdna_frequency,
-                    heterozygous: query_gnomad_mtdna_heteroplasmic,
-                    homozygous: query_gnomad_mtdna_homoplasmic,
+                    heteroplasmic: query_gnomad_mtdna_heteroplasmic,
+                    homoplasmic: query_gnomad_mtdna_homoplasmic,
                     ..Default::default()
                 },
                 ..Default::default()
@@ -533,10 +551,10 @@ mod test {
         };
         let seq_var = VariantRecord {
             population_frequencies: PopulationFrequencies {
-                gnomad_mt: MitochondrialFrequencies {
-                    an: seqvar_gnomad_genomes_an,
-                    het: seqvar_gnomad_genomes_het,
-                    hom: seqvar_gnomad_genomes_hom,
+                gnomad_mtdna: MitochondrialFrequencies {
+                    an: seqvar_gnomad_mtdna_an,
+                    het: seqvar_gnomad_mtdna_het,
+                    hom: seqvar_gnomad_mtdna_hom,
                     ..Default::default()
                 },
                 ..Default::default()
@@ -573,7 +591,13 @@ mod test {
             ..Default::default()
         };
 
-        assert_eq!(super::passes(&query, &seq_var)?, expected_pass_all);
+        assert_eq!(
+            super::passes(&query, &seq_var)?,
+            expected_pass_all,
+            "query: {:#?}, seq_var: {:#?}",
+            query,
+            seq_var
+        );
 
         Ok(())
     }
diff --git a/src/seqvars/query/interpreter/genotype.rs b/src/seqvars/query/interpreter/genotype.rs
index dc1a6213..98a4460b 100644
--- a/src/seqvars/query/interpreter/genotype.rs
+++ b/src/seqvars/query/interpreter/genotype.rs
@@ -1,20 +1,17 @@
 use crate::seqvars::query::schema::{
     data::VariantRecord,
     query::{
-        CaseQuery, GenotypeChoice, MatchesGenotypeStr as _, QuerySettingsGenotype, RecessiveMode,
+        considered_no_call, CaseQuery, GenotypeChoice, MatchesGenotypeStr as _,
+        QuerySettingsGenotype, RecessiveMode, RecessiveParents,
     },
 };
 
 /// Determine whether the `VariantRecord` passes the genotype filter.
-pub fn passes(
-    query: &CaseQuery,
-    seqvar: &VariantRecord,
-    no_call_samples: &[&str],
-) -> Result<bool, anyhow::Error> {
+pub fn passes(query: &CaseQuery, seqvar: &VariantRecord) -> Result<bool, anyhow::Error> {
     let result = if query.genotype.recessive_mode != RecessiveMode::Disabled {
-        passes_recessive_modes(&query.genotype, seqvar, no_call_samples)?
+        passes_recessive_modes(&query.genotype, seqvar)?
     } else {
-        passes_non_recessive_mode(&query.genotype, seqvar, no_call_samples)?
+        passes_non_recessive_mode(&query.genotype, seqvar)?
     };
 
     if !result {
@@ -28,157 +25,311 @@ pub fn passes(
 }
 
 /// Handle case of the mode being one of the recessive modes.
+///
+/// This means
+///
+/// - fail on chrMT/chrY
+/// - in case of chrX, require het./hom./hemi. in the index, het. in the mother and
+///   hom. ref. in the father
+/// - in case of autosomal chromosomes, require het. in index and exactly one parent
+///   and hom. ref. in other parent OR require hom. in index and het. in both parents
+///
+/// In the future, we could also provide the sex of the index here and include cases
+/// of X inactivation where mother is het., father is hom. ref. and index is het.
 fn passes_recessive_modes(
     query_genotype: &QuerySettingsGenotype,
     seqvar: &VariantRecord,
-    no_call_samples: &[&str],
 ) -> Result<bool, anyhow::Error> {
-    // Pick recessive index and parent names from query.
-    let index_name = query_genotype.recessive_index().map_err(|e| {
+    // Is/must never be called with disabled recessive mode.
+    assert_ne!(query_genotype.recessive_mode, RecessiveMode::Disabled);
+    // Get normalized chromosome, short-circuit in case of chrMT/chrY
+    // (recessive inheritance does not make sense here).
+    let normalized_chrom = annonars::common::cli::canonicalize(seqvar.vcf_variant.chrom.as_str());
+    if normalized_chrom == "MT" || normalized_chrom == "Y" {
+        tracing::trace!(
+            "variant {:?} fails for genotype filter {:?} (chrMT/chrY)",
+            seqvar,
+            query_genotype
+        );
+        return Ok(false);
+    }
+
+    // Extract genotypes of index and potentially mother/father.
+    let (index_gt, father_gt, mother_gt) = extract_trio_genotypes(query_genotype, seqvar)?;
+
+    // Branch into X-linked and autosomal recessive mode.
+    Ok(if normalized_chrom == "X" {
+        passes_recessive_mode_x_linked(index_gt, father_gt, mother_gt)
+    } else {
+        passes_recessive_mode_autosomal(
+            index_gt,
+            father_gt,
+            mother_gt,
+            query_genotype.recessive_mode,
+        )
+    })
+}
+
+/// Extract genotypes of index and potentially mother/father.
+///
+/// This function is used to extract the genotypes of the index and the parents
+///
+/// # Arguments
+///
+/// * `query_genotype` - The genotype filter to apply
+/// * `seqvar` - The variant record to check
+///
+/// # Returns
+///
+/// A tuple containing the genotypes of the index, father and mother
+///
+/// # Errors
+///
+/// This function returns an error if the parents names could not be extracted
+/// from the genotype query settings (more than one mother/father), if the
+/// index sample name could not be determined, or the genotypes of the family
+/// members could not be extracted from the variant record.
+fn extract_trio_genotypes<'a>(
+    query_genotype: &QuerySettingsGenotype,
+    seqvar: &'a VariantRecord,
+) -> Result<(&'a str, Option<&'a str>, Option<&'a str>), anyhow::Error> {
+    let index = query_genotype.recessive_index().map_err(|e| {
         anyhow::anyhow!(
             "invalid recessive index in genotype filter {:?}: {}",
             &query_genotype,
             e
         )
     })?;
-    let _parent_names = query_genotype.recessive_parents().map_err(|e| {
+    let RecessiveParents { father, mother } = query_genotype.recessive_parents().map_err(|e| {
         anyhow::anyhow!(
             "invalid recessive parents in genotype filter {:?}: {}",
             &query_genotype,
             e
         )
     })?;
-
-    // Get genotype choice of index.
-    let index_gt_choice = query_genotype
-        .sample_genotypes
-        .get(&index_name)
+    let index_gt = seqvar
+        .call_infos
+        .get(&index)
         .ok_or_else(|| {
-            anyhow::anyhow!(
-                "index sample {} not found in genotype filter {:?}",
-                &index_name,
-                &query_genotype
-            )
-        })?;
-    // For recessive mode, we have to know the samples selected for index and parents.
-    let index_gt_string = if no_call_samples.contains(&index_name.as_str()) {
-        String::from(".")
-    } else {
-        let call_info = seqvar.call_infos.get(&index_name).ok_or_else(|| {
             anyhow::anyhow!(
                 "index sample {} not found in call info for {:?}",
-                &index_name,
+                &index,
                 &seqvar
             )
-        })?;
-        call_info.genotype.as_ref().cloned().ok_or_else(|| {
+        })?
+        .genotype
+        .as_ref()
+        .ok_or_else(|| {
             anyhow::anyhow!(
                 "index sample {} has no genotype in call info for {:?}",
-                &index_name,
+                &index,
                 &seqvar
             )
         })?
-    };
-    let parent_names = query_genotype
-        .sample_genotypes
-        .iter()
-        .flat_map(|(sample, choice)| {
-            if choice.genotype == GenotypeChoice::RecessiveParent {
-                Some(sample.clone())
-            } else {
-                None
-            }
+        .as_str();
+    let father_gt = father
+        .map(|father| {
+            seqvar
+                .call_infos
+                .get(&father)
+                .ok_or_else(|| {
+                    anyhow::anyhow!(
+                        "father sample {} not found in call info for {:?}",
+                        &father,
+                        &seqvar
+                    )
+                })?
+                .genotype
+                .as_ref()
+                .ok_or_else(|| {
+                    anyhow::anyhow!(
+                        "father sample {} has no genotype in call info for {:?}",
+                        &father,
+                        &seqvar
+                    )
+                })
         })
-        .collect::<Vec<_>>();
-    let parent_gt_strings = parent_names
-        .iter()
-        .map(|parent_name| {
-            if no_call_samples.contains(&parent_name.as_str()) {
-                Ok(String::from(".")) // no-call
-            } else {
-                seqvar
-                    .call_infos
-                    .get(parent_name)
-                    .cloned()
-                    .ok_or_else(|| {
-                        anyhow::anyhow!(
-                            "parent sample {} not found in call info for {:?}",
-                            &parent_name,
-                            &seqvar
-                        )
-                    })?
-                    .genotype
-                    .ok_or_else(|| {
-                        anyhow::anyhow!(
-                            "parent sample {} has no genotype in call info for {:?}",
-                            &parent_name,
-                            &seqvar
-                        )
-                    })
-            }
+        .transpose()?
+        .map(|s| s.as_str());
+    let mother_gt = mother
+        .map(|mother| {
+            seqvar
+                .call_infos
+                .get(&mother)
+                .ok_or_else(|| {
+                    anyhow::anyhow!(
+                        "mother sample {} not found in call info for {:?}",
+                        &mother,
+                        &seqvar
+                    )
+                })?
+                .genotype
+                .as_ref()
+                .ok_or_else(|| {
+                    anyhow::anyhow!(
+                        "mother sample {} has no genotype in call info for {:?}",
+                        &mother,
+                        &seqvar
+                    )
+                })
         })
-        .collect::<Result<Vec<_>, _>>()?;
-
-    let compound_recessive_ok_index = GenotypeChoice::Het.matches(&index_gt_string);
-    let compound_recessive_parents_ref = parent_gt_strings
-        .iter()
-        .filter(|parent_gt_string| GenotypeChoice::Ref.matches(parent_gt_string))
-        .count();
-    let compound_recessive_parents_het = parent_gt_strings
-        .iter()
-        .filter(|parent_gt_string| GenotypeChoice::Het.matches(parent_gt_string))
-        .count();
-    let compound_recessive_parents_hom = parent_gt_strings
-        .iter()
-        .filter(|parent_gt_string| GenotypeChoice::Hom.matches(parent_gt_string))
-        .count();
-
-    let compound_recessive_ok = match parent_names.len() {
-        0 => compound_recessive_ok_index,
-        1 => {
-            compound_recessive_ok_index
-                && compound_recessive_parents_ref + compound_recessive_parents_het == 1
-                && compound_recessive_parents_hom == 0
+        .transpose()?
+        .map(|s| s.as_str());
+    Ok((index_gt, father_gt, mother_gt))
+}
+
+/// Handle case of the mode being "recessive" on chromosome X.
+fn passes_recessive_mode_x_linked(
+    index_gt: &str,
+    father_gt: Option<&str>,
+    mother_gt: Option<&str>,
+) -> bool {
+    if GenotypeChoice::Hom
+        .matches(index_gt)
+        .expect("matches() cannot fail for Hom")
+    {
+        // Index is hemi. alt.
+        //
+        // If father/mother is missing, we assume them to have compatible genotypes.
+        let father_ref = father_gt
+            .map(|father_gt| {
+                GenotypeChoice::Ref
+                    .matches(father_gt)
+                    .expect("matches() cannot fail for Ref")
+            })
+            .unwrap_or(true);
+        let mother_het = mother_gt
+            .map(|mother_gt| {
+                GenotypeChoice::Het
+                    .matches(mother_gt)
+                    .expect("matches() cannot fail for Het")
+            })
+            .unwrap_or(true);
+        father_ref && mother_het
+    } else {
+        false
+    }
+}
+
+/// Handle case of the mode being "recessive" on autosomal chromosomes.
+fn passes_recessive_mode_autosomal(
+    index_gt: &str,
+    father_gt: Option<&str>,
+    mother_gt: Option<&str>,
+    mode: RecessiveMode,
+) -> bool {
+    // Is/must never be called with disabled recessive mode.
+    assert_ne!(mode, RecessiveMode::Disabled);
+
+    if GenotypeChoice::Hom
+        .matches(index_gt)
+        .expect("matches() cannot fail for Hom")
+    {
+        // Index is hom. alt.
+        //
+        // Fail if in comp. het. mode.
+        if mode == RecessiveMode::CompoundHeterozygous {
+            return false;
         }
-        2 => {
-            compound_recessive_ok_index
-                && compound_recessive_parents_ref == 1
-                && compound_recessive_parents_het == 1
-                && compound_recessive_parents_hom == 0
+        assert!(matches!(
+            mode,
+            RecessiveMode::Any | RecessiveMode::Homozygous
+        ));
+        // Both parents must be het. if given.
+        let father_matches_het = father_gt
+            .map(|father_gt| {
+                GenotypeChoice::Het
+                    .matches(father_gt)
+                    .expect("matches() cannot fail for Het")
+            })
+            .unwrap_or(true);
+        let mother_matches_het = mother_gt
+            .map(|mother_gt| {
+                GenotypeChoice::Het
+                    .matches(mother_gt)
+                    .expect("matches() cannot fail for Het")
+            })
+            .unwrap_or(true);
+        father_matches_het && mother_matches_het
+    } else if GenotypeChoice::Het
+        .matches(&index_gt)
+        .expect("matches() cannot fail for Het")
+    {
+        // Index is het.
+        //
+        // Fail if in hom. mode.
+        if mode == RecessiveMode::Homozygous {
+            return false;
         }
-        _ => anyhow::bail!("more than two recessive parents selected"),
-    };
-
-    let homozygous_recessive_ok_index = GenotypeChoice::Hom.matches(&index_gt_string);
-    let homozygous_recessive_ok_parents = parent_gt_strings
-        .iter()
-        .map(|parent_gt_string| GenotypeChoice::Het.matches(parent_gt_string))
-        .collect::<Vec<_>>();
-    let homozygous_recessive_ok =
-        homozygous_recessive_ok_index && homozygous_recessive_ok_parents.iter().all(|&ok| ok);
-
-    match query_genotype.recessive_mode {
-        RecessiveMode::CompoundHeterozygous => Ok(compound_recessive_ok),
-        RecessiveMode::Homozygous => Ok(homozygous_recessive_ok),
-        RecessiveMode::Any => Ok(compound_recessive_ok || homozygous_recessive_ok),
-        _ => anyhow::bail!(
-            "invalid recessive mode choice for recessive mode: {:?}",
-            index_gt_choice
-        ),
+        assert!(matches!(
+            mode,
+            RecessiveMode::Any | RecessiveMode::CompoundHeterozygous
+        ));
+        // Exactly one parent must be het., the other hom. ref.  This means
+        // when counting het./ref. alleles, each sum must be <= 1.
+        let (hom_father, het_father, ref_father) = father_gt
+            .map(|father_gt| {
+                (
+                    GenotypeChoice::Hom
+                        .matches(father_gt)
+                        .expect("matches() cannot fail for Hom") as i32,
+                    GenotypeChoice::Het
+                        .matches(father_gt)
+                        .expect("matches() cannot fail for Het") as i32,
+                    GenotypeChoice::Ref
+                        .matches(father_gt)
+                        .expect("matches() cannot fail for Ref") as i32,
+                )
+            })
+            .unwrap_or((0, 0, 0));
+        let (hom_mother, het_mother, ref_mother) = mother_gt
+            .map(|mother_gt| {
+                (
+                    GenotypeChoice::Hom
+                        .matches(mother_gt)
+                        .expect("matches() cannot fail for Hom") as i32,
+                    GenotypeChoice::Het
+                        .matches(mother_gt)
+                        .expect("matches() cannot fail for Het") as i32,
+                    GenotypeChoice::Ref
+                        .matches(mother_gt)
+                        .expect("matches() cannot fail for Ref") as i32,
+                )
+            })
+            .unwrap_or((0, 0, 0));
+        (hom_father + hom_mother == 0)
+            && (het_father + het_mother <= 1)
+            && (ref_father + ref_mother <= 1)
+    } else {
+        // None of the inclusion criteria met.
+        false
     }
 }
 
-/// Handle case if the mode is not "recessive".  Note that this actually includes the
-/// homozygous recessive mode.
+/// Handle case if the mode is not "recessive".
+///
+/// Note that this includes the homozygous recessive mode.
+///
+/// # Arguments
+///
+/// * `query_genotype` - The genotype filter to apply
+/// * `seqvar` - The variant record to check
+///
+/// # Returns
+///
+/// A boolean indicating whether the variant passes the genotype filter
+///
+/// # Errors
+///
+/// This function returns an error if the genotype choice from the settings
+/// could not be matched with the genotype (e.g., is recessive indicator).
 fn passes_non_recessive_mode(
     query_genotype: &QuerySettingsGenotype,
     seqvar: &VariantRecord,
-    no_call_samples: &[&str],
 ) -> Result<bool, anyhow::Error> {
     for (sample_name, genotype_choice) in query_genotype.sample_genotypes.iter() {
-        let genotype = if no_call_samples.contains(&sample_name.as_str()) {
-            "." // no-call
-        } else if let Some(call_info) = seqvar.call_infos.get(sample_name) {
+        // Extract genotype from call info, skip if not present.
+        let genotype = if let Some(call_info) = seqvar.call_infos.get(sample_name) {
             if let Some(genotype) = call_info.genotype.as_ref() {
                 genotype
             } else {
@@ -190,7 +341,21 @@ fn passes_non_recessive_mode(
             return Ok(false);
         };
 
-        if !genotype_choice.genotype.matches(genotype) {
+        if considered_no_call(genotype) {
+            // Handle case of nocall genotype.
+            if genotype_choice.include_no_call {
+                continue;
+            } else {
+                tracing::trace!(
+                    "variant {:?} fails genotype filter {:?} on sample {} (no call)",
+                    seqvar,
+                    &query_genotype,
+                    sample_name
+                );
+                return Ok(false);
+            }
+        } else if !genotype_choice.genotype.matches(genotype)? {
+            // Handle case of non-nocall genotype.
             tracing::trace!(
                 "variant {:?} fails genotype filter {:?} on sample {}",
                 seqvar,
@@ -198,15 +363,17 @@ fn passes_non_recessive_mode(
                 sample_name
             );
             return Ok(false);
+        } else {
+            // All good, check next.
         }
     }
 
-    Ok(true) // all good up to here
+    Ok(true) // All good up to the end.
 }
 
 #[cfg(test)]
 mod test {
-    use crate::seqvars::query::schema::data::{CallInfo, VariantRecord};
+    use crate::seqvars::query::schema::data::{CallInfo, VariantRecord, VcfVariant};
     use crate::seqvars::query::schema::query::{
         GenotypeChoice::{self, *},
         QuerySettingsGenotype, RecessiveMode, SampleGenotypeChoice,
@@ -218,98 +385,118 @@ mod test {
 
     #[rstest::rstest]
     // any: passes
-    #[case("0/0", Any, true)]
-    #[case("0|0", Any, true)]
-    #[case("0/1", Any, true)]
-    #[case("0|1", Any, true)]
-    #[case("0", Any, true)]
-    #[case("1/0", Any, true)]
-    #[case("1|0", Any, true)]
-    #[case("1/1", Any, true)]
-    #[case("1|1", Any, true)]
-    #[case("1", Any, true)]
-    #[case(".", Any, true)]
-    #[case("./.", Any, true)]
-    #[case(".|.", Any, true)]
+    #[case::any_pass_01("0/0", Any, false, true)]
+    #[case::any_pass_02("0|0", Any, false, true)]
+    #[case::any_pass_03("0/1", Any, false, true)]
+    #[case::any_pass_04("0|1", Any, false, true)]
+    #[case::any_pass_05("0", Any, false, true)]
+    #[case::any_pass_06("1/0", Any, false, true)]
+    #[case::any_pass_07("1|0", Any, false, true)]
+    #[case::any_pass_08("1/1", Any, false, true)]
+    #[case::any_pass_09("1|1", Any, false, true)]
+    #[case::any_pass_10("1", Any, false, true)]
+    #[case::any_pass_11(".", Any, true, true)]
+    #[case::any_pass_12("./.", Any, true, true)]
+    #[case::any_pass_13(".|.", Any, true, true)]
+    // any: passes NOT
+    #[case::any_nopass_01(".", Any, false, false)]
+    #[case::any_nopass_02("./.", Any, false, false)]
+    #[case::any_nopass_03(".|.", Any, false, false)]
     // ref: passes
-    #[case("0/0", Ref, true)]
-    #[case("0|0", Ref, true)]
-    #[case("0", Ref, true)]
+    #[case::ref_pass_01("0/0", Ref, false, true)]
+    #[case::ref_pass_02("0|0", Ref, false, true)]
+    #[case::ref_pass_03("0", Ref, false, true)]
+    #[case::ref_pass_04(".", Ref, true, true)]
+    #[case::ref_pass_05("./.", Ref, true, true)]
+    #[case::ref_pass_06(".|.", Ref, true, true)]
     // ref: passes NOT
-    #[case("0/1", Ref, false)]
-    #[case("0|1", Ref, false)]
-    #[case("1/0", Ref, false)]
-    #[case("1|0", Ref, false)]
-    #[case("1/1", Ref, false)]
-    #[case("1|1", Ref, false)]
-    #[case("1", Ref, false)]
-    #[case(".", Ref, false)]
-    #[case("./.", Ref, false)]
-    #[case(".|.", Ref, false)]
+    #[case::ref_nopass_01("0/1", Ref, false, false)]
+    #[case::ref_nopass_02("0|1", Ref, false, false)]
+    #[case::ref_nopass_03("1/0", Ref, false, false)]
+    #[case::ref_nopass_04("1|0", Ref, false, false)]
+    #[case::ref_nopass_05("1/1", Ref, false, false)]
+    #[case::ref_nopass_06("1|1", Ref, false, false)]
+    #[case::ref_nopass_07("1", Ref, false, false)]
+    #[case::ref_nopass_08(".", Ref, false, false)]
+    #[case::ref_nopass_09("./.", Ref, false, false)]
+    #[case::ref_nopass_10(".|.", Ref, false, false)]
     // het: passes
-    #[case("0/1", Het, true)]
-    #[case("0|1", Het, true)]
-    #[case("1/0", Het, true)]
-    #[case("1|0", Het, true)]
+    #[case::het_pass_01("0/1", Het, false, true)]
+    #[case::het_pass_02("0|1", Het, false, true)]
+    #[case::het_pass_03("1/0", Het, false, true)]
+    #[case::het_pass_04("1|0", Het, false, true)]
+    #[case::het_pass_05(".", Het, true, true)]
+    #[case::het_pass_06("./.", Het, true, true)]
+    #[case::het_pass_07(".|.", Het, true, true)]
     // het: passes NOT
-    #[case("0/0", Het, false)]
-    #[case("0|0", Het, false)]
-    #[case("0", Het, false)]
-    #[case("1/1", Het, false)]
-    #[case("1|1", Het, false)]
-    #[case("1", Het, false)]
-    #[case(".", Het, false)]
-    #[case("./.", Het, false)]
-    #[case(".|.", Het, false)]
+    #[case::het_nopass_01("0/0", Het, false, false)]
+    #[case::het_nopass_02("0|0", Het, false, false)]
+    #[case::het_nopass_03("0", Het, false, false)]
+    #[case::het_nopass_04("1/1", Het, false, false)]
+    #[case::het_nopass_05("1|1", Het, false, false)]
+    #[case::het_nopass_06("1", Het, false, false)]
+    #[case::het_nopass_07(".", Het, false, false)]
+    #[case::het_nopass_08("./.", Het, false, false)]
+    #[case::het_nopass_09(".|.", Het, false, false)]
     // hom: passes
-    #[case("1/1", Hom, true)]
-    #[case("1|1", Hom, true)]
-    #[case("1", Hom, true)]
+    #[case::hom_pass_01("1/1", Hom, false, true)]
+    #[case::hom_pass_02("1|1", Hom, false, true)]
+    #[case::hom_pass_03("1", Hom, false, true)]
+    #[case::hom_pass_04(".", Hom, true, true)]
+    #[case::hom_pass_05("./.", Hom, true, true)]
+    #[case::hom_pass_06(".|.", Hom, true, true)]
     // hom: passes NOT
-    #[case("0/0", Hom, false)]
-    #[case("0|0", Hom, false)]
-    #[case("0/1", Hom, false)]
-    #[case("0|1", Hom, false)]
-    #[case("0", Hom, false)]
-    #[case("1/0", Hom, false)]
-    #[case("1|0", Hom, false)]
-    #[case(".", Hom, false)]
-    #[case("./.", Hom, false)]
-    #[case(".|.", Hom, false)]
+    #[case::hom_nopass_01("0/0", Hom, false, false)]
+    #[case::hom_nopass_02("0|0", Hom, false, false)]
+    #[case::hom_nopass_03("0/1", Hom, false, false)]
+    #[case::hom_nopass_04("0|1", Hom, false, false)]
+    #[case::hom_nopass_05("0", Hom, false, false)]
+    #[case::hom_nopass_06("1/0", Hom, false, false)]
+    #[case::hom_nopass_07("1|0", Hom, false, false)]
+    #[case::hom_nopass_08(".", Hom, false, false)]
+    #[case::hom_nopass_09("./.", Hom, false, false)]
+    #[case::hom_nopass_10(".|.", Hom, false, false)]
     // non-hom: passes
-    #[case("0/0", NonHom, true)]
-    #[case("0|0", NonHom, true)]
-    #[case("0/1", NonHom, true)]
-    #[case("0|1", NonHom, true)]
-    #[case("0", NonHom, true)]
-    #[case("1/0", NonHom, true)]
-    #[case("1|0", NonHom, true)]
-    #[case(".", NonHom, true)]
-    #[case("./.", NonHom, true)]
-    #[case(".|.", NonHom, true)]
+    #[case::nonhom_pass_01("0/0", NonHom, false, true)]
+    #[case::nonhom_pass_02("0|0", NonHom, false, true)]
+    #[case::nonhom_pass_03("0/1", NonHom, false, true)]
+    #[case::nonhom_pass_04("0|1", NonHom, false, true)]
+    #[case::nonhom_pass_05("0", NonHom, false, true)]
+    #[case::nonhom_pass_06("1/0", NonHom, false, true)]
+    #[case::nonhom_pass_07("1|0", NonHom, false, true)]
+    #[case::nonhom_pass_08(".", NonHom, true, true)]
+    #[case::nonhom_pass_09("./.", NonHom, true, true)]
+    #[case::nonhom_pass_10(".|.", NonHom, true, true)]
     // non-hom: passes NOT
-    #[case("1/1", NonHom, false)]
-    #[case("1|1", NonHom, false)]
-    #[case("1", NonHom, false)]
+    #[case::nonhom_nopass_01("1/1", NonHom, false, false)]
+    #[case::nonhom_nopass_02("1|1", NonHom, false, false)]
+    #[case::nonhom_nopass_03("1", NonHom, false, false)]
+    #[case::nonhom_nopass_04(".", NonHom, false, false)]
+    #[case::nonhom_nopass_05("./.", NonHom, false, false)]
+    #[case::nonhom_nopass_06(".|.", NonHom, false, false)]
     // variant: passes
-    #[case("0/1", Variant, true)]
-    #[case("0|1", Variant, true)]
-    #[case("1/0", Variant, true)]
-    #[case("1|0", Variant, true)]
-    #[case("1/1", Variant, true)]
-    #[case("1|1", Variant, true)]
-    #[case("1", Variant, true)]
+    #[case::variant_pass_01("0/1", Variant, false, true)]
+    #[case::variant_pass_02("0|1", Variant, false, true)]
+    #[case::variant_pass_03("1/0", Variant, false, true)]
+    #[case::variant_pass_04("1|0", Variant, false, true)]
+    #[case::variant_pass_05("1/1", Variant, false, true)]
+    #[case::variant_pass_06("1|1", Variant, false, true)]
+    #[case::variant_pass_07("1", Variant, false, true)]
+    #[case::variant_pass_08(".", Variant, true, true)]
+    #[case::variant_pass_09("./.", Variant, true, true)]
+    #[case::variant_pass_10(".|.", Variant, true, true)]
     // variant: passes NOT
-    #[case("0/0", Variant, false)]
-    #[case("0|0", Variant, false)]
-    #[case("0", Variant, false)]
-    #[case(".", Variant, false)]
-    #[case("./.", Variant, false)]
-    #[case(".|.", Variant, false)]
+    #[case::variant_nopass_01("0/0", Variant, false, false)]
+    #[case::variant_nopass_02("0|0", Variant, false, false)]
+    #[case::variant_nopass_03("0", Variant, false, false)]
+    #[case::variant_nopass_04(".", Variant, false, false)]
+    #[case::variant_nopass_05("./.", Variant, false, false)]
+    #[case::variant_nopass_06(".|.", Variant, false, false)]
 
     fn passes_non_recessive_mode_singleton(
         #[case] sample_gt: &str,
         #[case] query_gt: GenotypeChoice,
+        #[case] include_no_call: bool,
         #[case] expected: bool,
     ) -> Result<(), anyhow::Error> {
         let query_genotype = QuerySettingsGenotype {
@@ -318,6 +505,7 @@ mod test {
                 String::from(INDEX_NAME) => SampleGenotypeChoice {
                     sample: String::from(INDEX_NAME),
                     genotype: query_gt,
+                    include_no_call,
                     ..Default::default()
                 }
             },
@@ -335,7 +523,7 @@ mod test {
         };
 
         assert_eq!(
-            super::passes_non_recessive_mode(&query_genotype, &seq_var, &[])?,
+            super::passes_non_recessive_mode(&query_genotype, &seq_var)?,
             expected,
             "sample_gt = {}, query_gt = {:?}, expected = {}",
             sample_gt,
@@ -348,32 +536,35 @@ mod test {
 
     #[rstest::rstest]
     // any: passes
-    #[case("0/0,0/0,0/0", Any, Any, Any, true)]
-    #[case(".,.,.", Any, Any, Any, true)]
+    #[case::any_pass_01("0/0,0/0,0/0", Any, false, Any, false, Any, false, true)]
+    #[case::any_pass_01(".,.,.", Any, true, Any, true, Any, true, true)]
     // some combinations: passes
-    #[case("0/1,0/1,0/0", Het, Het, Ref, true)]
-    #[case("0/1,0|1,0/0", Het, Het, Ref, true)]
-    #[case("0|1,0/1,0/0", Het, Het, Ref, true)]
-    #[case("0/1,0/0,0/1", Any, Ref, Het, true)]
-    #[case("0|1,0/0,0|1", Any, Ref, Het, true)]
-    #[case("0/1,0/0,0|1", Any, Ref, Het, true)]
-    #[case("0|1,0/0,0/1", Any, Ref, Het, true)]
-    #[case("0/1,0/0,0/0", Variant, Ref, Ref, true)]
-    #[case("0|1,0/0,0/0", Variant, Ref, Ref, true)]
-    #[case("1/0,0/0,0/0", Variant, Ref, Ref, true)]
-    #[case("1|0,0/0,0/0", Variant, Ref, Ref, true)]
-    #[case("1,0,0/0", Variant, Ref, Ref, true)]
+    #[case::some_pass_01("0/1,0/1,0/0", Het, false, Het, false, Ref, false, true)]
+    #[case::some_pass_02("0/1,0|1,0/0", Het, false, Het, false, Ref, false, true)]
+    #[case::some_pass_03("0|1,0/1,0/0", Het, false, Het, false, Ref, false, true)]
+    #[case::some_pass_04("0/1,0/0,0/1", Any, false, Ref, false, Het, false, true)]
+    #[case::some_pass_05("0|1,0/0,0|1", Any, false, Ref, false, Het, false, true)]
+    #[case::some_pass_06("0/1,0/0,0|1", Any, false, Ref, false, Het, false, true)]
+    #[case::some_pass_07("0|1,0/0,0/1", Any, false, Ref, false, Het, false, true)]
+    #[case::some_pass_08("0/1,0/0,0/0", Variant, false, Ref, false, Ref, false, true)]
+    #[case::some_pass_09("0|1,0/0,0/0", Variant, false, Ref, false, Ref, false, true)]
+    #[case::some_pass_10("1/0,0/0,0/0", Variant, false, Ref, false, Ref, false, true)]
+    #[case::some_pass_11("1|0,0/0,0/0", Variant, false, Ref, false, Ref, false, true)]
+    #[case::some_pass_12("1,0,0/0", Variant, false, Ref, false, Ref, false, true)]
     // some combinations: passes NOT
-    #[case("0/0,0/0,0/0", Het, Any, Any, false)]
-    #[case("0/0,0/0,0/0", Any, Het, Any, false)]
-    #[case("0/0,0/0,0/0", Any, Any, Het, false)]
-    #[case("1,0,0/1", Variant, Ref, Ref, false)]
-    #[case("1,0,.", Variant, Ref, Ref, false)]
+    #[case::some_nopass_01("0/0,0/0,0/0", Het, false, Any, false, Any, false, false)]
+    #[case::some_nopass_02("0/0,0/0,0/0", Any, false, Het, false, Any, false, false)]
+    #[case::some_nopass_03("0/0,0/0,0/0", Any, false, Any, false, Het, false, false)]
+    #[case::some_nopass_04("1,0,0/1", Variant, false, Ref, false, Ref, false, false)]
+    #[case::some_nopass_05("1,0,.", Variant, false, Ref, false, Ref, false, false)]
     fn passes_non_recessive_mode_trio(
         #[case] sample_gts: &str,
         #[case] query_gt_index: GenotypeChoice,
+        #[case] nocall_index: bool,
         #[case] query_gt_father: GenotypeChoice,
+        #[case] nocall_father: bool,
         #[case] query_gt_mother: GenotypeChoice,
+        #[case] nocall_mother: bool,
         #[case] expected: bool,
     ) -> Result<(), anyhow::Error> {
         let query_genotype = QuerySettingsGenotype {
@@ -382,16 +573,19 @@ mod test {
                 String::from(INDEX_NAME) => SampleGenotypeChoice {
                     sample: String::from(INDEX_NAME),
                     genotype: query_gt_index,
+                    include_no_call: nocall_index,
                     ..Default::default()
                 },
                 String::from(FATHER_NAME) => SampleGenotypeChoice {
                     sample: String::from(FATHER_NAME),
                     genotype: query_gt_father,
+                    include_no_call: nocall_father,
                     ..Default::default()
                 },
                 String::from(MOTHER_NAME) => SampleGenotypeChoice {
                     sample: String::from(MOTHER_NAME),
                     genotype: query_gt_mother,
+                    include_no_call: nocall_mother,
                     ..Default::default()
                 },
             },
@@ -422,7 +616,7 @@ mod test {
         };
 
         assert_eq!(
-            super::passes_non_recessive_mode(&query_genotype, &seq_var, &[])?,
+            super::passes_non_recessive_mode(&query_genotype, &seq_var)?,
             expected,
             "sample_gt = {:?}, query_gt_index = {:?}, query_gt_father = {:?}, \
             query_gt_mother = {:?}, expected = {}",
@@ -437,9 +631,9 @@ mod test {
     }
 
     #[rstest::rstest]
-    // any: passes
-    #[case("0/0", RecessiveIndex)]
-    #[case("0/0", RecessiveParent)]
+    #[case::recessive_index("0/0", RecessiveIndex)]
+    #[case::recessive_father("0/0", RecessiveFather)]
+    #[case::recessive_mother("0/0", RecessiveMother)]
     fn passes_non_recessive_mode_fails_on_recessive_markers(
         #[case] sample_gt: &str,
         #[case] query_gt: GenotypeChoice,
@@ -465,53 +659,68 @@ mod test {
             ..Default::default()
         };
 
-        assert!(super::passes_non_recessive_mode(&query_genotype, &seq_var, &[]).is_err(),);
+        assert!(super::passes_non_recessive_mode(&query_genotype, &seq_var).is_err(),);
 
         Ok(())
     }
 
     #[rstest::rstest]
-    // // comphet-index: passes
-    // #[case("0/1", ComphetIndex, true)]
-    // #[case("0|1", ComphetIndex, true)]
-    // #[case("1/0", ComphetIndex, true)]
-    // #[case("1|0", ComphetIndex, true)]
-    // // comphet-index: passes NOT
-    // #[case("0/0", ComphetIndex, false)]
-    // #[case("0|0", ComphetIndex, false)]
-    // #[case("0", ComphetIndex, false)]
-    // #[case("1/1", ComphetIndex, false)]
-    // #[case("1|1", ComphetIndex, false)]
-    // #[case("1", ComphetIndex, false)]
-    // #[case(".", ComphetIndex, false)]
-    // #[case("./.", ComphetIndex, false)]
-    // #[case(".|.", ComphetIndex, false)]
-    // recessive-index: passes
-    #[case("0/1", RecessiveIndex, true)]
-    #[case("0|1", RecessiveIndex, true)]
-    #[case("1/0", RecessiveIndex, true)]
-    #[case("1|0", RecessiveIndex, true)]
-    #[case("1/1", RecessiveIndex, true)]
-    #[case("1|1", RecessiveIndex, true)]
-    #[case("1", RecessiveIndex, true)]
-    // recessive-index: passes NOT
-    #[case("0/0", RecessiveIndex, false)]
-    #[case("0|0", RecessiveIndex, false)]
-    #[case("0", RecessiveIndex, false)]
-    #[case(".", RecessiveIndex, false)]
-    #[case("./.", RecessiveIndex, false)]
-    #[case(".|.", RecessiveIndex, false)]
-    fn passes_recessive_modes_singleton(
+    // any: passes
+    #[case::any_pass_01("0/1", RecessiveMode::Any, true)]
+    #[case::any_pass_02("0|1", RecessiveMode::Any, true)]
+    #[case::any_pass_03("1/0", RecessiveMode::Any, true)]
+    #[case::any_pass_04("1|0", RecessiveMode::Any, true)]
+    #[case::any_pass_05("1/1", RecessiveMode::Any, true)]
+    #[case::any_pass_06("1|1", RecessiveMode::Any, true)]
+    #[case::any_pass_07("1", RecessiveMode::Any, true)]
+    // any: passes NOT
+    #[case::any_nopass_01("0/0", RecessiveMode::Any, false)]
+    #[case::any_nopass_02("0|0", RecessiveMode::Any, false)]
+    #[case::any_nopass_03("0", RecessiveMode::Any, false)]
+    #[case::any_nopass_04(".", RecessiveMode::Any, false)]
+    #[case::any_nopass_05("./.", RecessiveMode::Any, false)]
+    #[case::any_nopass_06(".|.", RecessiveMode::Any, false)]
+    // comp. het.: passes
+    #[case::comphet_pass_01("0/1", RecessiveMode::CompoundHeterozygous, true)]
+    #[case::comphet_pass_02("0|1", RecessiveMode::CompoundHeterozygous, true)]
+    #[case::comphet_pass_03("1/0", RecessiveMode::CompoundHeterozygous, true)]
+    #[case::comphet_pass_04("1|0", RecessiveMode::CompoundHeterozygous, true)]
+    // comp. het.: passes NOT
+    #[case::comphet_nopass_01("0/0", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_02("0|0", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_03("0", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_04("1/1", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_05("1|1", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_06("1", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_07(".", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_08("./.", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_09(".|.", RecessiveMode::CompoundHeterozygous, false)]
+    // hom.: passes
+    #[case::hom_pass_04("1/1", RecessiveMode::Homozygous, true)]
+    #[case::hom_pass_05("1|1", RecessiveMode::Homozygous, true)]
+    #[case::hom_pass_06("1", RecessiveMode::Homozygous, true)]
+    // hom.: passes NOT
+    #[case::hom_nopass_01("0/0", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_02("0|0", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_03("0", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_04("0/1", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_05("0|1", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_06("1/0", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_07("1|0", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_08(".", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_09("./.", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_10(".|.", RecessiveMode::Homozygous, false)]
+    fn passes_recessive_modes_autosomes_singleton(
         #[case] sample_gt: &str,
-        #[case] query_gt: GenotypeChoice,
+        #[case] recessive_mode: RecessiveMode,
         #[case] expected: bool,
     ) -> Result<(), anyhow::Error> {
         let query_genotype = QuerySettingsGenotype {
-            recessive_mode: RecessiveMode::Any,
+            recessive_mode,
             sample_genotypes: indexmap::indexmap! {
                 String::from(INDEX_NAME) => SampleGenotypeChoice {
                     sample: String::from(INDEX_NAME),
-                    genotype: query_gt,
+                    genotype: GenotypeChoice::RecessiveIndex,
                     ..Default::default()
                 }
             },
@@ -528,11 +737,11 @@ mod test {
         };
 
         assert_eq!(
-            super::passes_recessive_modes(&query_genotype, &seq_var, &[])?,
+            super::passes_recessive_modes(&query_genotype, &seq_var)?,
             expected,
-            "sample_gt = {}, query_gt = {:?}, expected = {}",
+            "sample_gt = {}, recessive_mode = {:?}, expected = {}",
             sample_gt,
-            query_gt,
+            recessive_mode,
             expected
         );
 
@@ -540,48 +749,463 @@ mod test {
     }
 
     #[rstest::rstest]
-    // recessive mode: passes
-    #[case("0/1,0/0,0/0", RecessiveIndex, Any, Any, true)]
-    #[case("0|1,0/0,0/0", RecessiveIndex, Any, Any, true)]
-    #[case("1/0,0/0,0/0", RecessiveIndex, Any, Any, true)]
-    #[case("1|0,0/0,0/0", RecessiveIndex, Any, Any, true)]
-    #[case("1/0,0/1,0/0", RecessiveIndex, RecessiveParent, RecessiveParent, true)]
-    #[case("1/0,0/0,0/1", RecessiveIndex, RecessiveParent, RecessiveParent, true)]
-    #[case("1/1,0/1,0/1", RecessiveIndex, RecessiveParent, RecessiveParent, true)]
-    #[case("1/1,0/0,0/1", RecessiveIndex, Any, RecessiveParent, true)]
-    #[case("1/1,0/1,0/0", RecessiveIndex, RecessiveParent, Any, true)]
-    #[case("1|1,0|1,1|0", RecessiveIndex, RecessiveParent, RecessiveParent, true)]
-    // recessive mode: passes NOT
-    #[case("1/1,1/1,0/0", RecessiveIndex, RecessiveParent, Any, false)]
-    #[case("0/1,0/0,0/0", RecessiveIndex, RecessiveParent, RecessiveParent, false)]
-    #[case("0/1,1/1,0/0", RecessiveIndex, RecessiveParent, RecessiveParent, false)]
-    #[case("0/1,0/0,1/1", RecessiveIndex, RecessiveParent, RecessiveParent, false)]
-    #[case("0/1,0/1,0/1", RecessiveIndex, RecessiveParent, RecessiveParent, false)]
-    // // compound recessive mode: passes
-    // #[case("0/1,0/0,0/0", ComphetIndex, Any, Any, true)]
-    // #[case("0|1,0/0,0/0", ComphetIndex, Any, Any, true)]
-    // #[case("1/0,0/0,0/0", ComphetIndex, Any, Any, true)]
-    // #[case("1|0,0/0,0/0", ComphetIndex, Any, Any, true)]
-    // #[case("0/1,1/1,0/0", ComphetIndex, Any, RecessiveParent, true)]
-    // #[case("0/1,0/0,1/1", ComphetIndex, RecessiveParent, Any, true)]
-    // #[case("1/0,0/1,0/0", ComphetIndex, RecessiveParent, RecessiveParent, true)]
-    // #[case("1/0,0/0,0/1", ComphetIndex, RecessiveParent, RecessiveParent, true)]
-    // // compound recessive mode: passes NOT
-    // #[case("1/1,0/1,0/1", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    // #[case("1|1,0|1,1|0", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    // #[case("0/1,0/0,0/0", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    // #[case("0/1,1/1,0/0", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    // #[case("0/1,0/0,1/1", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    // #[case("0/1,0/1,0/1", ComphetIndex, RecessiveParent, RecessiveParent, false)]
-    fn passes_recessive_modes_trio(
+    // any: passes
+    #[case::any_pass_01("1/1", RecessiveMode::Any, true)]
+    #[case::any_pass_02("1|1", RecessiveMode::Any, true)]
+    #[case::any_pass_03("1", RecessiveMode::Any, true)]
+    // any: passes NOT
+    #[case::any_nopass_01("0/1", RecessiveMode::Any, false)]
+    #[case::any_nopass_02("0|1", RecessiveMode::Any, false)]
+    #[case::any_nopass_03("1/0", RecessiveMode::Any, false)]
+    #[case::any_nopass_04("1|0", RecessiveMode::Any, false)]
+    #[case::any_nopass_05("0/0", RecessiveMode::Any, false)]
+    #[case::any_nopass_06("0|0", RecessiveMode::Any, false)]
+    #[case::any_nopass_07("0", RecessiveMode::Any, false)]
+    #[case::any_nopass_08(".", RecessiveMode::Any, false)]
+    #[case::any_nopass_09("./.", RecessiveMode::Any, false)]
+    #[case::any_nopass_10(".|.", RecessiveMode::Any, false)]
+    // comp. het.: passes
+    // recessive mode is ignored -- sic!
+    #[case::comphet_pass_01("1/1", RecessiveMode::CompoundHeterozygous, true)]
+    #[case::comphet_pass_02("1|1", RecessiveMode::CompoundHeterozygous, true)]
+    #[case::comphet_pass_03("1", RecessiveMode::CompoundHeterozygous, true)]
+    // comp. het.: passes NOT
+    #[case::comphet_nopass_01("0/1", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_02("0|1", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_03("1/0", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_04("1|0", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_05("0/0", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_06("0|0", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_07("0", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_08(".", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_09("./.", RecessiveMode::CompoundHeterozygous, false)]
+    #[case::comphet_nopass_10(".|.", RecessiveMode::CompoundHeterozygous, false)]
+    // hom.: passes
+    #[case::hom_pass_04("1/1", RecessiveMode::Homozygous, true)]
+    #[case::hom_pass_05("1|1", RecessiveMode::Homozygous, true)]
+    #[case::hom_pass_06("1", RecessiveMode::Homozygous, true)]
+    // hom.: passes NOT
+    #[case::hom_nopass_01("0/0", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_02("0|0", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_03("0", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_04("0/1", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_05("0|1", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_06("1/0", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_07("1|0", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_08(".", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_09("./.", RecessiveMode::Homozygous, false)]
+    #[case::hom_nopass_10(".|.", RecessiveMode::Homozygous, false)]
+    fn passes_recessive_modes_x_linked_singleton(
+        #[case] sample_gt: &str,
+        #[case] recessive_mode: RecessiveMode,
+        #[case] expected: bool,
+    ) -> Result<(), anyhow::Error> {
+        let query_genotype = QuerySettingsGenotype {
+            recessive_mode,
+            sample_genotypes: indexmap::indexmap! {
+                String::from(INDEX_NAME) => SampleGenotypeChoice {
+                    sample: String::from(INDEX_NAME),
+                    genotype: GenotypeChoice::RecessiveIndex,
+                    ..Default::default()
+                }
+            },
+        };
+        let seq_var = VariantRecord {
+            vcf_variant: VcfVariant {
+                chrom: "X".to_string(),
+                ..Default::default()
+            },
+            call_infos: indexmap::indexmap! {
+                INDEX_NAME.into() =>
+                CallInfo {
+                    genotype: Some(sample_gt.into()),
+                    ..Default::default()
+                },
+            },
+            ..Default::default()
+        };
+
+        assert_eq!(
+            super::passes_recessive_modes(&query_genotype, &seq_var)?,
+            expected,
+            "sample_gt = {}, recessive_mode = {:?}, expected = {}",
+            sample_gt,
+            recessive_mode,
+            expected
+        );
+
+        Ok(())
+    }
+
+    #[rstest::rstest]
+    #[case::chry_any_fail("Y", "0/1", RecessiveMode::Any)]
+    #[case::chry_any_fail("Y", "1/1", RecessiveMode::Homozygous)]
+    #[case::chry_any_fail("Y", "0/1", RecessiveMode::CompoundHeterozygous)]
+    #[case::chrmt_any_fail("MT", "0/1", RecessiveMode::Any)]
+    #[case::chrmt_any_fail("MT", "1/1", RecessiveMode::Homozygous)]
+    #[case::chrmt_any_fail("MT", "0/1", RecessiveMode::CompoundHeterozygous)]
+    fn passes_recessive_modes_chry_chrmt_singleton(
+        #[case] chrom: &str,
+        #[case] sample_gt: &str,
+        #[case] recessive_mode: RecessiveMode,
+    ) -> Result<(), anyhow::Error> {
+        let query_genotype = QuerySettingsGenotype {
+            recessive_mode,
+            sample_genotypes: indexmap::indexmap! {
+                String::from(INDEX_NAME) => SampleGenotypeChoice {
+                    sample: String::from(INDEX_NAME),
+                    genotype: GenotypeChoice::RecessiveIndex,
+                    ..Default::default()
+                }
+            },
+        };
+        let seq_var = VariantRecord {
+            vcf_variant: VcfVariant {
+                chrom: chrom.to_string(),
+                ..Default::default()
+            },
+            call_infos: indexmap::indexmap! {
+                INDEX_NAME.into() =>
+                CallInfo {
+                    genotype: Some(sample_gt.into()),
+                    ..Default::default()
+                },
+            },
+            ..Default::default()
+        };
+
+        assert_eq!(
+            super::passes_recessive_modes(&query_genotype, &seq_var)?,
+            false,
+            "sample_gt = {}, recessive_mode = {:?}",
+            sample_gt,
+            recessive_mode,
+        );
+
+        Ok(())
+    }
+
+    #[rstest::rstest]
+    // any recessive mode: passes
+    #[case::any_pass_01("0/1,0/0,0/0", RecessiveIndex, Any, Any, RecessiveMode::Any, true)]
+    #[case::any_pass_02("0|1,0/0,0/0", RecessiveIndex, Any, Any, RecessiveMode::Any, true)]
+    #[case::any_pass_03("1/0,0/0,0/0", RecessiveIndex, Any, Any, RecessiveMode::Any, true)]
+    #[case::any_pass_04("1|0,0/0,0/0", RecessiveIndex, Any, Any, RecessiveMode::Any, true)]
+    #[case::any_pass_05(
+        "1/0,0/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        true
+    )]
+    #[case::any_pass_06(
+        "1/0,0/0,0/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        true
+    )]
+    #[case::any_pass_07(
+        "1/1,0/1,0/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        true
+    )]
+    #[case::any_pass_08(
+        "1/1,0/0,0/1",
+        RecessiveIndex,
+        Any,
+        RecessiveMother,
+        RecessiveMode::Any,
+        true
+    )]
+    #[case::any_pass_09(
+        "1/1,0/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        Any,
+        RecessiveMode::Any,
+        true
+    )]
+    #[case::any_pass_10(
+        "1|1,0|1,1|0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        true
+    )]
+    // any recessive mode: passes NOT
+    #[case::any_nopass_01(
+        "1/1,1/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        Any,
+        RecessiveMode::Any,
+        false
+    )]
+    #[case::any_nopass_02(
+        "0/1,0/0,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        false
+    )]
+    #[case::any_nopass_03(
+        "0/1,1/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        false
+    )]
+    #[case::any_nopass_04(
+        "0/1,0/0,1/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        false
+    )]
+    #[case::any_nopass_05(
+        "0/1,0/1,0/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        false
+    )]
+    // homozygous recessive mode: passes
+    #[case::homozygous_pass_01(
+        "1/1,0/1,0/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Homozygous,
+        true
+    )]
+    #[case::homozygous_pass_02(
+        "1/1,0/0,0/1",
+        RecessiveIndex,
+        Any,
+        RecessiveMother,
+        RecessiveMode::Homozygous,
+        true
+    )]
+    #[case::homozygous_pass_03(
+        "1/1,0/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        Any,
+        RecessiveMode::Homozygous,
+        true
+    )]
+    #[case::homozygous_pass_04(
+        "1|1,0|1,1|0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Homozygous,
+        true
+    )]
+    // homozygous recessive mode: passes NOT
+    #[case::homozygous_pass_01(
+        "0/1,0/0,0/0",
+        RecessiveIndex,
+        Any,
+        Any,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    #[case::homozygous_pass_02(
+        "0|1,0/0,0/0",
+        RecessiveIndex,
+        Any,
+        Any,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    #[case::homozygous_pass_03(
+        "1/0,0/0,0/0",
+        RecessiveIndex,
+        Any,
+        Any,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    #[case::homozygous_pass_04(
+        "1|0,0/0,0/0",
+        RecessiveIndex,
+        Any,
+        Any,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    #[case::homozygous_pass_05(
+        "1/0,0/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    #[case::homozygous_pass_06(
+        "1/0,0/0,0/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    #[case::homozygous_pass_07(
+        "1/1,1/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        Any,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    #[case::homozygous_pass_08(
+        "0/1,0/0,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    #[case::homozygous_pass_09(
+        "0/1,1/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    #[case::homozygous_pass_10(
+        "0/1,0/0,1/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    #[case::homozygous_pass_11(
+        "0/1,0/1,0/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Homozygous,
+        false
+    )]
+    // comp. het. recessive mode: passes
+    #[case::comphet_pass_01("0/1,0/0,0/0", RecessiveIndex, Any, Any, RecessiveMode::Any, true)]
+    #[case::comphet_pass_02("0|1,0/0,0/0", RecessiveIndex, Any, Any, RecessiveMode::Any, true)]
+    #[case::comphet_pass_03("1/0,0/0,0/0", RecessiveIndex, Any, Any, RecessiveMode::Any, true)]
+    #[case::comphet_pass_04("1|0,0/0,0/0", RecessiveIndex, Any, Any, RecessiveMode::Any, true)]
+    #[case::comphet_pass_05(
+        "1/0,0/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        true
+    )]
+    #[case::comphet_pass_06(
+        "1/0,0/0,0/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        true
+    )]
+    #[case::comphet_pass_07(
+        "1/1,0/1,0/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        true
+    )]
+    #[case::comphet_pass_08(
+        "1/1,0/0,0/1",
+        RecessiveIndex,
+        Any,
+        RecessiveMother,
+        RecessiveMode::Any,
+        true
+    )]
+    #[case::comphet_pass_09(
+        "1/1,0/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        Any,
+        RecessiveMode::Any,
+        true
+    )]
+    #[case::comphet_pass_10(
+        "1|1,0|1,1|0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        true
+    )]
+    // comp. het. recessive mode: passes NOT
+    #[case::comphet_nopass_01(
+        "1/1,1/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        Any,
+        RecessiveMode::Any,
+        false
+    )]
+    #[case::comphet_nopass_02(
+        "0/1,0/0,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        false
+    )]
+    #[case::comphet_nopass_03(
+        "0/1,1/1,0/0",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        false
+    )]
+    #[case::comphet_nopass_04(
+        "0/1,0/0,1/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        false
+    )]
+    #[case::comphet_nopass_05(
+        "0/1,0/1,0/1",
+        RecessiveIndex,
+        RecessiveFather,
+        RecessiveMother,
+        RecessiveMode::Any,
+        false
+    )]
+    fn passes_recessive_modes_autosomes_trio(
         #[case] sample_gts: &str,
         #[case] query_gt_index: GenotypeChoice,
         #[case] query_gt_father: GenotypeChoice,
         #[case] query_gt_mother: GenotypeChoice,
+        #[case] recessive_mode: RecessiveMode,
         #[case] expected: bool,
     ) -> Result<(), anyhow::Error> {
         let query_genotype = QuerySettingsGenotype {
-            recessive_mode: RecessiveMode::Any,
+            recessive_mode,
             sample_genotypes: indexmap::indexmap! {
                 String::from(INDEX_NAME) => SampleGenotypeChoice {
                     sample: String::from(INDEX_NAME),
@@ -626,14 +1250,15 @@ mod test {
         };
 
         assert_eq!(
-            super::passes_recessive_modes(&query_genotype, &seq_var, &[])?,
+            super::passes_recessive_modes(&query_genotype, &seq_var)?,
             expected,
             "sample_gt = {:?}, query_gt_index = {:?}, query_gt_father = {:?}, \
-            query_gt_mother = {:?}, expected = {}",
+            query_gt_mother = {:?}, recessive_mode = {:?}, expected = {}",
             sample_gts,
             query_gt_index,
             query_gt_father,
             query_gt_mother,
+            recessive_mode,
             expected
         );
 
diff --git a/src/seqvars/query/interpreter/mod.rs b/src/seqvars/query/interpreter/mod.rs
index 8ea2a9a7..9e172902 100644
--- a/src/seqvars/query/interpreter/mod.rs
+++ b/src/seqvars/query/interpreter/mod.rs
@@ -50,29 +50,19 @@ impl QueryInterpreter {
         // Check the filters first that are cheap to compute.
         let pass_frequency = frequency::passes(&self.query, seqvar)?;
         let pass_consequences = consequences::passes(&self.query, seqvar)?;
-        let res_quality = quality::passes(&self.query, seqvar)?;
+        let pass_quality = quality::passes(&self.query, seqvar)?;
         let pass_genes_allowlist = genes_allowlist::passes(&self.hgnc_allowlist, seqvar);
         let pass_regions_allowlist = regions_allowlist::passes(&self.query, seqvar);
+        let pass_genotype = genotype::passes(&self.query, seqvar)?;
         if !pass_frequency
             || !pass_consequences
-            || !res_quality.pass
+            || !pass_quality
             || !pass_genes_allowlist
             || !pass_regions_allowlist
+            || !pass_genotype
         {
             return Ok(PassesResult { pass_all: false });
         }
-        // Now also check the genotype that needs the quality filter output as input.
-        if !genotype::passes(
-            &self.query,
-            seqvar,
-            &res_quality
-                .no_call_samples
-                .iter()
-                .map(|s| s.as_str())
-                .collect::<Vec<_>>(),
-        )? {
-            return Ok(PassesResult { pass_all: false });
-        }
         // If we passed until here, check the presence in ClinVar which needs a database lookup.
         Ok(PassesResult {
             pass_all: clinvar::passes(&self.query, annotator, seqvar)?,
diff --git a/src/seqvars/query/interpreter/quality.rs b/src/seqvars/query/interpreter/quality.rs
index 196938ac..d7b1a1cf 100644
--- a/src/seqvars/query/interpreter/quality.rs
+++ b/src/seqvars/query/interpreter/quality.rs
@@ -6,22 +6,9 @@ use crate::{
     },
 };
 
-/// Return type for the `passes` function.
-#[derive(Debug)]
-pub struct PassOrNoCall {
-    /// Whether the variant should be kept.
-    pub pass: bool,
-    /// For which samples should the genotype be interpreted as no-call.
-    pub no_call_samples: Vec<String>,
-}
-
 /// Determine whether the `VariantRecord` passes the quality filter.
 /// Will return `FailFilterChoice::Ignore` if the variant passes.
-pub fn passes(query: &CaseQuery, seqvar: &VariantRecord) -> Result<PassOrNoCall, anyhow::Error> {
-    let mut result = PassOrNoCall {
-        pass: true,
-        no_call_samples: Vec::new(),
-    };
+pub fn passes(query: &CaseQuery, seqvar: &VariantRecord) -> Result<bool, anyhow::Error> {
     for (sample_name, quality_settings) in &query.quality.sample_qualities {
         if let Some(call_info) = seqvar.call_infos.get(sample_name) {
             if !passes_for_sample(quality_settings, call_info) {
@@ -33,8 +20,12 @@ pub fn passes(query: &CaseQuery, seqvar: &VariantRecord) -> Result<PassOrNoCall,
                     &quality_settings
                 );
                 if quality_settings.filter_active {
-                    result.pass = false;
-                    break;
+                    tracing::trace!(
+                        "variant {:?} fails quality filter for sample {:?}",
+                        seqvar,
+                        &sample_name
+                    );
+                    return Ok(false);
                 }
             } else {
                 // no failure, all good
@@ -44,17 +35,17 @@ pub fn passes(query: &CaseQuery, seqvar: &VariantRecord) -> Result<PassOrNoCall,
         }
     }
 
-    tracing::trace!(
-        "variant {:?} has result {:?} for quality filter {:?}",
-        seqvar,
-        result,
-        &query.genotype
-    );
-    Ok(result)
+    tracing::trace!("variant {:?} passes quality filter", seqvar,);
+    Ok(true)
 }
 
 /// Return whether the sample passes the quality filter.
 fn passes_for_sample(quality_settings: &SampleQualitySettings, call_info: &CallInfo) -> bool {
+    // Short-circuit if the filter is not active.
+    if !quality_settings.filter_active {
+        return true;
+    }
+
     // Ad-hoc enum for genotype.
     #[derive(PartialEq, Eq)]
     enum Genotype {
@@ -143,15 +134,14 @@ mod test {
     };
 
     #[rstest::rstest]
-    #[case(false, true, true, false)]
-    #[case(false, false, true, false)]
-    #[case(true, true, true, false)]
-    #[case(true, false, false, false)]
+    #[case(false, true, true)]
+    #[case(false, false, true)]
+    #[case(true, true, true)]
+    #[case(true, false, false)]
     fn passes(
         #[case] filter_active: bool,
         #[case] should_pass: bool,
-        #[case] expected_pass: bool,
-        #[case] any_no_call_sample: bool,
+        #[case] expected: bool,
     ) -> Result<(), anyhow::Error> {
         let query = CaseQuery {
             quality: QuerySettingsQuality {
@@ -181,17 +171,7 @@ mod test {
         let res = super::passes(&query, &seqvar)?;
 
         assert_eq!(
-            res.pass, expected_pass,
-            "query = {:#?}, seqvar = {:#?}",
-            &query, &seqvar
-        );
-        let expected = if any_no_call_sample {
-            vec![String::from("sample")]
-        } else {
-            vec![]
-        };
-        assert_eq!(
-            &res.no_call_samples, &expected,
+            res, expected,
             "query = {:#?}, seqvar = {:#?}",
             &query, &seqvar
         );
@@ -477,7 +457,7 @@ mod test {
         assert_eq!(
             super::passes_for_sample(&settings, &call_info),
             expected,
-            "settings: {:?}, call info: {:?}",
+            "settings: {:#?}, call info: {:#?}",
             settings,
             call_info
         );
diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs
index e20c31c8..7430416d 100644
--- a/src/seqvars/query/mod.rs
+++ b/src/seqvars/query/mod.rs
@@ -100,7 +100,7 @@ fn passes_for_gene(query: &CaseQuery, seqvars: &Vec<VariantRecord>) -> Result<bo
                 GenotypeChoice::RecessiveIndex => {
                     index.clone_from(sample_name);
                 }
-                GenotypeChoice::RecessiveParent => {
+                GenotypeChoice::RecessiveFather | GenotypeChoice::RecessiveMother => {
                     parents.push(sample_name.clone());
                 }
                 _ => (),
@@ -607,8 +607,8 @@ mod test {
                 recessive_mode,
                 sample_genotypes: indexmap::indexmap! {
                     String::from("index") => SampleGenotypeChoice { sample: String::from("index"), genotype: GenotypeChoice::RecessiveIndex, ..Default::default() },
-                    String::from("father") => SampleGenotypeChoice { sample: String::from("father"), genotype: GenotypeChoice::RecessiveParent, ..Default::default() },
-                    String::from("mother") => SampleGenotypeChoice { sample: String::from("mother"), genotype: GenotypeChoice::RecessiveParent, ..Default::default() },
+                    String::from("father") => SampleGenotypeChoice { sample: String::from("father"), genotype: GenotypeChoice::RecessiveFather, ..Default::default() },
+                    String::from("mother") => SampleGenotypeChoice { sample: String::from("mother"), genotype: GenotypeChoice::RecessiveMother, ..Default::default() },
                 },
             },
             ..Default::default()
diff --git a/src/seqvars/query/output/variant_related.rs b/src/seqvars/query/output/variant_related.rs
index 22459433..ac834107 100644
--- a/src/seqvars/query/output/variant_related.rs
+++ b/src/seqvars/query/output/variant_related.rs
@@ -420,10 +420,10 @@ impl Frequency {
             FrequencyBuilder::default()
                 .gnomad_mtdna(
                     MtdnaFrequency::new(
-                        seqvar.population_frequencies.gnomad_mt.af(),
-                        seqvar.population_frequencies.gnomad_mt.ac(),
-                        seqvar.population_frequencies.gnomad_mt.het(),
-                        seqvar.population_frequencies.gnomad_mt.hom(),
+                        seqvar.population_frequencies.gnomad_mtdna.af(),
+                        seqvar.population_frequencies.gnomad_mtdna.ac(),
+                        seqvar.population_frequencies.gnomad_mtdna.het(),
+                        seqvar.population_frequencies.gnomad_mtdna.hom(),
                     )
                     .some_unless_empty(),
                 )
diff --git a/src/seqvars/query/schema/data.rs b/src/seqvars/query/schema/data.rs
index 7a3aa9f5..065f9e8e 100644
--- a/src/seqvars/query/schema/data.rs
+++ b/src/seqvars/query/schema/data.rs
@@ -205,7 +205,7 @@ impl An for InHouseFrequencies {
 
 impl Carriers for InHouseFrequencies {
     fn carriers(&self) -> i32 {
-        2 * self.hom + self.het + self.hemi
+        self.hom + self.het + self.hemi
     }
 }
 
@@ -217,7 +217,7 @@ pub struct PopulationFrequencies {
     /// Frequencies in gnomAD-genomes.
     pub gnomad_genomes: NuclearFrequencies,
     /// Frequencies in gnomAD-MT.
-    pub gnomad_mt: MitochondrialFrequencies,
+    pub gnomad_mtdna: MitochondrialFrequencies,
     /// Frequencies in HelixMtDb.
     pub helixmtdb: MitochondrialFrequencies,
     /// Frequencies in In-house database.
@@ -284,7 +284,7 @@ impl TryFromVcf for PopulationFrequencies {
                 het: gnomad_genomes_het,
                 hemi: gnomad_genomes_hemi,
             },
-            gnomad_mt: MitochondrialFrequencies {
+            gnomad_mtdna: MitochondrialFrequencies {
                 an: gnomad_mtdna_an,
                 hom: gnomad_mtdna_hom,
                 het: gnomad_mtdna_het,
@@ -608,7 +608,7 @@ mod tests {
         PopulationFrequencies {
             gnomad_exomes: nuclear_frequencies.clone(),
             gnomad_genomes: nuclear_frequencies.clone(),
-            gnomad_mt: mitochondrial_frequencies.clone(),
+            gnomad_mtdna: mitochondrial_frequencies.clone(),
             helixmtdb: mitochondrial_frequencies.clone(),
             inhouse: inhouse_frequencies.clone(),
         }
@@ -681,14 +681,14 @@ mod tests {
     fn test_population_frequencies(population_frequencies: PopulationFrequencies) {
         assert_eq!(population_frequencies.gnomad_exomes.an, 100);
         assert_eq!(population_frequencies.gnomad_genomes.an, 100);
-        assert_eq!(population_frequencies.gnomad_mt.an, 100);
+        assert_eq!(population_frequencies.gnomad_mtdna.an, 100);
         assert_eq!(population_frequencies.helixmtdb.an, 100);
         assert_eq!(population_frequencies.inhouse.total, 35);
     }
 
     #[rstest::rstest]
-    #[case("tests/seqvars/query/Case_1.ingested.vcf")]
-    #[case("tests/seqvars/query/dragen.ingested.vcf")]
+    #[case::case_1_ingested_vcf("tests/seqvars/query/Case_1.ingested.vcf")]
+    #[case::dragen_ingested_vcf("tests/seqvars/query/dragen.ingested.vcf")]
     pub fn sequence_variant_from_vcf(#[case] path_input: &str) -> Result<(), anyhow::Error> {
         use noodles::vcf::variant::RecordBuf;
 
diff --git a/src/seqvars/query/schema/query.rs b/src/seqvars/query/schema/query.rs
index cec2a4f6..0cbdcbfc 100644
--- a/src/seqvars/query/schema/query.rs
+++ b/src/seqvars/query/schema/query.rs
@@ -90,22 +90,31 @@ pub enum GenotypeChoice {
     Variant,
     /// Recessive index.
     RecessiveIndex,
-    /// Recessive parent.
-    RecessiveParent,
+    /// Recessive father.
+    RecessiveFather,
+    /// Recessive mother.
+    RecessiveMother,
 }
 
 /// Supporting code for `GenotypeChoice`.
 pub(crate) mod genotype_choice {
     /// Error type for `GenotypeChoice::try_from()`.
     #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
-    pub enum Error {
+    pub enum TryFromError {
         #[error("Cannot convert protobuf GenotypeChoice: {0:?}")]
         UnknownGenotypeChoiceValue(super::pb_query::GenotypeChoice),
     }
+
+    /// Error type for `GenotypeChoice::matches()`.
+    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
+    pub enum MatchesError {
+        #[error("Cannot use genotype matches on recessive indicator: {0:?}")]
+        RecessiveIndicator(super::GenotypeChoice),
+    }
 }
 
 impl TryFrom<pb_query::GenotypeChoice> for GenotypeChoice {
-    type Error = genotype_choice::Error;
+    type Error = genotype_choice::TryFromError;
 
     fn try_from(value: pb_query::GenotypeChoice) -> Result<Self, Self::Error> {
         match value {
@@ -117,20 +126,32 @@ impl TryFrom<pb_query::GenotypeChoice> for GenotypeChoice {
             pb_query::GenotypeChoice::NonHom => Ok(GenotypeChoice::NonHom),
             pb_query::GenotypeChoice::Variant => Ok(GenotypeChoice::Variant),
             pb_query::GenotypeChoice::RecessiveIndex => Ok(GenotypeChoice::RecessiveIndex),
-            pb_query::GenotypeChoice::RecessiveParent => Ok(GenotypeChoice::RecessiveParent),
+            pb_query::GenotypeChoice::RecessiveFather => Ok(GenotypeChoice::RecessiveFather),
+            pb_query::GenotypeChoice::RecessiveMother => Ok(GenotypeChoice::RecessiveMother),
             _ => Err(Self::Error::UnknownGenotypeChoiceValue(value)),
         }
     }
 }
 
+/// Returns whether the given genotype script is treated as no-call.
+///
+/// This is the case if the genotype string contains at least one ".".
+pub fn considered_no_call(gt_str: &str) -> bool {
+    gt_str.contains('.')
+}
+
 /// Trait that describes whether a string matches a value.
 ///
 /// Note that we assume properly ingested VCFs with only one alternate allele.
 /// The valid genotype strings have the form "<VAL>/<VAL>", "<VAL>|<VAL>" or
 /// "<VAL>" with "<VAL>" being one of "0", "1", and ".".
 pub trait MatchesGenotypeStr {
+    type Error;
+
     /// Whether `self` matches `s`.
     ///
+    /// Note that no-call genotypes do not match anything.
+    ///
     /// # Arguments
     ///
     /// * `gt_str` - The string to match against.
@@ -138,29 +159,47 @@ pub trait MatchesGenotypeStr {
     /// # Returns
     ///
     /// `true` if `self` matches `gt_str`, `false` otherwise.
-    fn matches(&self, gt_tr: &str) -> bool;
+    ///
+    /// # Errors
+    ///
+    /// * When the conversion fails.
+    fn matches(&self, gt_tr: &str) -> Result<bool, Self::Error>;
 }
 
 impl MatchesGenotypeStr for GenotypeChoice {
-    fn matches(&self, gt_str: &str) -> bool {
+    type Error = genotype_choice::MatchesError;
+
+    fn matches(&self, gt_str: &str) -> Result<bool, Self::Error> {
         let gt_str = if gt_str.starts_with('/') || gt_str.starts_with('|') {
             &gt_str[1..]
         } else {
             gt_str
         };
-        match self {
-            GenotypeChoice::Any => true,
+        Ok(match self {
+            // atoms
             GenotypeChoice::Ref => ["0", "0|0", "0/0"].contains(&gt_str),
-            GenotypeChoice::RecessiveIndex
-            | GenotypeChoice::RecessiveParent
-            | GenotypeChoice::Het => ["0/1", "0|1", "1/0", "1|0"].contains(&gt_str),
+            GenotypeChoice::Het => ["0/1", "0|1", "1/0", "1|0"].contains(&gt_str),
             GenotypeChoice::Hom => ["1", "1/1", "1|1"].contains(&gt_str),
-            GenotypeChoice::NonHom => !["1", "1/1", "1|1"].contains(&gt_str),
-            GenotypeChoice::NonHet => !["0/1", "0|1", "1/0", "1|0"].contains(&gt_str),
+            // combinations
             GenotypeChoice::Variant => {
-                ["1", "0/1", "0|1", "1/0", "1|0", "1|1", "1/1"].contains(&gt_str)
+                GenotypeChoice::Het.matches(gt_str)? || GenotypeChoice::Hom.matches(gt_str)?
             }
-        }
+            GenotypeChoice::Any => {
+                GenotypeChoice::Ref.matches(gt_str)? || GenotypeChoice::Variant.matches(gt_str)?
+            }
+            GenotypeChoice::NonHom => {
+                GenotypeChoice::Ref.matches(gt_str)? || GenotypeChoice::Het.matches(gt_str)?
+            }
+            GenotypeChoice::NonHet => {
+                GenotypeChoice::Ref.matches(gt_str)? || GenotypeChoice::Hom.matches(gt_str)?
+            }
+            // recessive markers
+            GenotypeChoice::RecessiveIndex
+            | GenotypeChoice::RecessiveFather
+            | GenotypeChoice::RecessiveMother => {
+                return Err(Self::Error::RecessiveIndicator(*self))
+            }
+        })
     }
 }
 
@@ -239,8 +278,10 @@ pub(crate) mod query_settings_genotype {
     /// Error type for `QuerySettingsGenotype::recessive_parents()`.
     #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
     pub enum RecessiveParentsError {
-        #[error("Too many recessive parent samples found: {0:?}")]
-        TooManyRecessiveParentsFound(Vec<String>),
+        #[error("Found two or more recessive fathers: {0:?}")]
+        Fathers(Vec<String>),
+        #[error("Found two or more recessive mothers: {0:?}")]
+        Mothers(Vec<String>),
     }
 
     /// Error type for `QuerySettingsGenotype::try_from()`.
@@ -257,6 +298,28 @@ pub(crate) mod query_settings_genotype {
     }
 }
 
+/// Struct for storing recessive mother/father.
+#[derive(Debug, Clone, Default, PartialEq, Eq, serde::Serialize, serde::Deserialize)]
+pub struct RecessiveParents {
+    /// Name of the father, if any.
+    pub father: Option<String>,
+    /// Name of the mother, if any.
+    pub mother: Option<String>,
+}
+
+impl Into<Vec<String>> for RecessiveParents {
+    fn into(self) -> Vec<String> {
+        let mut result = Vec::new();
+        if let Some(father) = self.father {
+            result.push(father);
+        }
+        if let Some(mother) = self.mother {
+            result.push(mother);
+        }
+        result
+    }
+}
+
 impl QuerySettingsGenotype {
     /// Return the selected recessive index sample.
     ///
@@ -292,29 +355,43 @@ impl QuerySettingsGenotype {
     ///
     /// # Returns
     ///
-    /// The sample names of the recessive parent samples (zero to two).
+    /// Struct holding names of recessive father and mother, if any.
     ///
     /// # Errors
     ///
-    /// * `RecessiveParentsError::TooManyRecessiveParentsFound` if more than two recessive parent samples are found.
+    /// * `RecessiveParentsError::Fathers` or `RecessiveParentsError::Mothers` if more than two
+    ///   recessive fathers/mothers samples are found.
     pub fn recessive_parents(
         &self,
-    ) -> Result<Vec<String>, query_settings_genotype::RecessiveParentsError> {
-        let samples = self
+    ) -> Result<RecessiveParents, query_settings_genotype::RecessiveParentsError> {
+        let fathers = self
             .sample_genotypes
             .values()
-            .filter(|sgc| sgc.genotype == GenotypeChoice::RecessiveParent)
+            .filter(|sgc| matches!(sgc.genotype, GenotypeChoice::RecessiveFather))
             .map(|sgc| sgc.sample.clone())
             .collect::<Vec<_>>();
-        if samples.len() > 2 {
-            Err(
-                query_settings_genotype::RecessiveParentsError::TooManyRecessiveParentsFound(
-                    samples,
-                ),
-            )
-        } else {
-            Ok(samples)
+        if fathers.len() > 2 {
+            return Err(query_settings_genotype::RecessiveParentsError::Fathers(
+                fathers,
+            ));
+        }
+
+        let mothers = self
+            .sample_genotypes
+            .values()
+            .filter(|sgc| matches!(sgc.genotype, GenotypeChoice::RecessiveMother))
+            .map(|sgc| sgc.sample.clone())
+            .collect::<Vec<_>>();
+        if mothers.len() > 2 {
+            return Err(query_settings_genotype::RecessiveParentsError::Mothers(
+                mothers,
+            ));
         }
+
+        Ok(RecessiveParents {
+            father: fathers.into_iter().next(),
+            mother: mothers.into_iter().next(),
+        })
     }
 }
 
@@ -530,8 +607,8 @@ pub struct QuerySettingsFrequency {
     pub gnomad_exomes: GnomadNuclearFrequencySettings,
     /// gnomAD-genomes filter.
     pub gnomad_genomes: GnomadNuclearFrequencySettings,
-    /// gnomAD-MT filter.
-    pub gnomad_mt: GnomadMitochondrialFrequencySettings,
+    /// gnomAD-mtDNA filter.
+    pub gnomad_mtdna: GnomadMitochondrialFrequencySettings,
     /// HelixMtDb filter.
     pub helixmtdb: HelixMtDbFrequencySettings,
     /// In-house filter.
@@ -547,8 +624,8 @@ pub(crate) mod query_settings_frequency {
         GnomadExomes,
         #[error("gnomad_genomes missing in protobuf")]
         GnomadGenomes,
-        #[error("gnomad_mt missing in protobuf")]
-        GnomadMt,
+        #[error("gnomad_mtdna missing in protobuf")]
+        GnomadMtdna,
         #[error("helixmtdb missing in protobuf")]
         HelixMtDb,
         #[error("inhouse missing in protobuf")]
@@ -567,8 +644,8 @@ impl TryFrom<pb_query::QuerySettingsFrequency> for QuerySettingsFrequency {
             gnomad_genomes: GnomadNuclearFrequencySettings::from(
                 value.gnomad_genomes.ok_or(Self::Error::GnomadGenomes)?,
             ),
-            gnomad_mt: GnomadMitochondrialFrequencySettings::from(
-                value.gnomad_mt.ok_or(Self::Error::GnomadMt)?,
+            gnomad_mtdna: GnomadMitochondrialFrequencySettings::from(
+                value.gnomad_mtdna.ok_or(Self::Error::GnomadMtdna)?,
             ),
             helixmtdb: HelixMtDbFrequencySettings::from(
                 value.helixmtdb.ok_or(Self::Error::HelixMtDb)?,
@@ -1199,6 +1276,28 @@ mod tests {
 
     use super::*;
 
+    #[rstest::rstest]
+    #[case::dot(".", true)]
+    #[case::dot_slash_dot("./.", true)]
+    #[case::dot_pipe_dot(".|.", true)]
+    #[case::zero("0", false)]
+    #[case::zero_slash_dot("0/.", true)]
+    #[case::zero_pipe_dot("0|.", true)]
+    #[case::dot_slash_zero("./0", true)]
+    #[case::dot_pipe_zero(".|0", true)]
+    #[case::one("1", false)]
+    #[case::one_slash_dot("1/.", true)]
+    #[case::one_pipe_dot("1|.", true)]
+    #[case::dot_slash_one("./1", true)]
+    #[case::dot_pipe_one(".|1", true)]
+    #[case::zero_slash_one("0/1", false)]
+    #[case::zero_pipe_one("0|1", false)]
+    #[case::one_slash_zero("1/0", false)]
+    #[case::one_pipe_zero("1|0", false)]
+    fn test_considered_no_call(#[case] gt: &str, #[case] expected: bool) {
+        assert_eq!(super::considered_no_call(gt), expected);
+    }
+
     #[test]
     fn test_recessive_mode_try_from() {
         assert_eq!(
@@ -1255,8 +1354,12 @@ mod tests {
             GenotypeChoice::RecessiveIndex
         );
         assert_eq!(
-            GenotypeChoice::try_from(pb_query::GenotypeChoice::RecessiveParent).unwrap(),
-            GenotypeChoice::RecessiveParent
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::RecessiveFather).unwrap(),
+            GenotypeChoice::RecessiveFather
+        );
+        assert_eq!(
+            GenotypeChoice::try_from(pb_query::GenotypeChoice::RecessiveMother).unwrap(),
+            GenotypeChoice::RecessiveMother
         );
         assert!(GenotypeChoice::try_from(pb_query::GenotypeChoice::Unspecified).is_err());
     }
@@ -1300,18 +1403,20 @@ mod tests {
             #[case] genotype_choice: GenotypeChoice,
             #[case] gt_strs: &[&str],
             #[case] expected: bool,
-        ) {
+        ) -> Result<(), anyhow::Error> {
             use crate::seqvars::query::schema::query::MatchesGenotypeStr as _;
 
             for gt_str in gt_strs {
                 assert_eq!(
-                    genotype_choice.matches(gt_str),
+                    genotype_choice.matches(gt_str)?,
                     expected,
                     "{:?} {}",
                     genotype_choice,
                     gt_str
                 );
             }
+
+            Ok(())
         }
     }
 
@@ -1579,7 +1684,7 @@ mod tests {
                 hemizygous: Some(30),
                 frequency: Some(0.1),
             }),
-            gnomad_mt: Some(pb_query::GnomadMitochondrialFrequencySettings {
+            gnomad_mtdna: Some(pb_query::GnomadMitochondrialFrequencySettings {
                 enabled: true,
                 heteroplasmic: Some(10),
                 homoplasmic: Some(20),
@@ -1614,7 +1719,7 @@ mod tests {
                 hemizygous: Some(30),
                 frequency: Some(0.1),
             },
-            gnomad_mt: GnomadMitochondrialFrequencySettings {
+            gnomad_mtdna: GnomadMitochondrialFrequencySettings {
                 enabled: true,
                 heteroplasmic: Some(10),
                 homoplasmic: Some(20),
@@ -2007,7 +2112,7 @@ mod tests {
                     hemizygous: Some(30),
                     frequency: Some(0.1),
                 }),
-                gnomad_mt: Some(pb_query::GnomadMitochondrialFrequencySettings {
+                gnomad_mtdna: Some(pb_query::GnomadMitochondrialFrequencySettings {
                     enabled: true,
                     heteroplasmic: Some(10),
                     homoplasmic: Some(20),
@@ -2118,7 +2223,7 @@ mod tests {
                     hemizygous: Some(30),
                     frequency: Some(0.1),
                 },
-                gnomad_mt: GnomadMitochondrialFrequencySettings {
+                gnomad_mtdna: GnomadMitochondrialFrequencySettings {
                     enabled: true,
                     heteroplasmic: Some(10),
                     homoplasmic: Some(20),
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap
new file mode 100644
index 00000000..d4ce3142
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap
@@ -0,0 +1,203 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41273700
+  ref_allele: C
+  alt_allele: CA
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 42
+    dp: 14
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 10
+    dp: 7
+    ad: 1
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 65
+    dp: 10
+    ad: 5
+    phasing_id: ~
+ann_fields:
+  - allele:
+      Alt:
+        alternative: CA
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 2
+      total: 22
+    hgvs_t: c.80+2333_80+2334insT
+    hgvs_p: p.?
+    tx_pos:
+      ord: 193
+      total: 7088
+    cds_pos:
+      ord: 80
+      total: 5592
+    protein_pos: ~
+    distance: -2334
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: CA
+    consequences:
+      - 5_prime_UTR_intron_variant
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 2
+      total: 21
+    hgvs_t: c.-8+2333_-8+2334insT
+    hgvs_p: p.?
+    tx_pos:
+      ord: 187
+      total: 7028
+    cds_pos:
+      ord: -8
+      total: 5451
+    protein_pos: ~
+    distance: -2334
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: CA
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 1
+      total: 21
+    hgvs_t: c.80+2333_80+2334insT
+    hgvs_p: p.?
+    tx_pos:
+      ord: 99
+      total: 3682
+    cds_pos:
+      ord: 80
+      total: 2280
+    protein_pos: ~
+    distance: -2334
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: CA
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 2
+      total: 21
+    hgvs_t: c.80+2333_80+2334insT
+    hgvs_p: p.?
+    tx_pos:
+      ord: 187
+      total: 3696
+    cds_pos:
+      ord: 80
+      total: 2100
+    protein_pos: ~
+    distance: -2334
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: CA
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 2
+      total: 23
+    hgvs_t: c.80+2333_80+2334insT
+    hgvs_p: p.?
+    tx_pos:
+      ord: 193
+      total: 7151
+    cds_pos:
+      ord: 80
+      total: 5655
+    protein_pos: ~
+    distance: -2334
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap
new file mode 100644
index 00000000..b1a4c8c8
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 73
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3975
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2871
+    ad: 2871
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3320
+    ad: 3320
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap
new file mode 100644
index 00000000..93d1fae2
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 119
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 5418
+    ad: 1
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 4039
+    ad: 4039
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 4113
+    ad: 4112
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap
new file mode 100644
index 00000000..6362a4e5
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 189
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3069
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1721
+    ad: 1721
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2204
+    ad: 2204
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap
new file mode 100644
index 00000000..9eb3ac32
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 195
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2599
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1592
+    ad: 1592
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1815
+    ad: 1815
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap
new file mode 100644
index 00000000..7afee8ea
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 204
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2180
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1424
+    ad: 1424
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1304
+    ad: 1304
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap
new file mode 100644
index 00000000..c5e2ab09
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 207
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2115
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1408
+    ad: 1408
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1277
+    ad: 1277
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap
new file mode 100644
index 00000000..4a2c94e6
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 263
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1288
+    ad: 1288
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1204
+    ad: 1204
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1031
+    ad: 1031
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap
new file mode 100644
index 00000000..fbaa4638
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 302
+  ref_allele: A
+  alt_allele: ACC
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 844
+    ad: 687
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1011
+    ad: 6
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 803
+    ad: 3
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap
new file mode 100644
index 00000000..421621a7
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 310
+  ref_allele: T
+  alt_allele: TC
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1035
+    ad: 1035
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1411
+    ad: 1411
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1091
+    ad: 1090
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap
new file mode 100644
index 00000000..019cc199
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap
@@ -0,0 +1,202 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41252332
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 75
+    dp: 25
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 28
+    ad: 14
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 40
+    ad: 21
+    phasing_id: ~
+ann_fields:
+  - allele:
+      Alt:
+        alternative: C
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 6
+      total: 22
+    hgvs_t: c.442-435A>G
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7088
+    cds_pos:
+      ord: 442
+      total: 5592
+    protein_pos: ~
+    distance: 435
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: C
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.301-435A>G
+    hgvs_p: p.?
+    tx_pos:
+      ord: 495
+      total: 7028
+    cds_pos:
+      ord: 301
+      total: 5451
+    protein_pos: ~
+    distance: 435
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: C
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.442-435A>G
+    hgvs_p: p.?
+    tx_pos:
+      ord: 461
+      total: 3682
+    cds_pos:
+      ord: 442
+      total: 2280
+    protein_pos: ~
+    distance: 435
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: C
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 21
+    hgvs_t: c.442-435A>G
+    hgvs_p: p.?
+    tx_pos:
+      ord: 549
+      total: 3696
+    cds_pos:
+      ord: 442
+      total: 2100
+    protein_pos: ~
+    distance: 435
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: C
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 23
+    hgvs_t: c.442-435A>G
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7151
+    cds_pos:
+      ord: 442
+      total: 5655
+    protein_pos: ~
+    distance: 435
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap
new file mode 100644
index 00000000..5681548c
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 477
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2133
+    ad: 2129
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2267
+    ad: 1
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1725
+    ad: 0
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap
new file mode 100644
index 00000000..9ee2e85c
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 709
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2494
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2186
+    ad: 2186
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1814
+    ad: 1813
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap
new file mode 100644
index 00000000..7bbf606e
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 750
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2757
+    ad: 2757
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2392
+    ad: 2392
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1621
+    ad: 1621
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap
new file mode 100644
index 00000000..cfcfa2f9
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 879
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2853
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2784
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 1898
+    ad: 547
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap
new file mode 100644
index 00000000..1b6b4303
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 1243
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2675
+    ad: 1
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2198
+    ad: 2198
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1655
+    ad: 1655
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap
new file mode 100644
index 00000000..3b5ae0e8
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 1438
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3815
+    ad: 3815
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3653
+    ad: 3653
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2900
+    ad: 2900
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap
new file mode 100644
index 00000000..b553d222
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 1824
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2668
+    ad: 2668
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2409
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1752
+    ad: 0
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap
new file mode 100644
index 00000000..b42db030
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 2633
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2535
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 2409
+    ad: 761
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2269
+    ad: 0
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap
new file mode 100644
index 00000000..95e59a31
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 2706
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3200
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2847
+    ad: 2847
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2020
+    ad: 2020
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap
new file mode 100644
index 00000000..0b9f496b
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 3010
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2841
+    ad: 2841
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2385
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1685
+    ad: 0
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap
new file mode 100644
index 00000000..e756d7e2
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap
@@ -0,0 +1,202 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41252691
+  ref_allele: ATATAAT
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 27
+    dp: 9
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 14
+    ad: 10
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 23
+    ad: 11
+    phasing_id: ~
+ann_fields:
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 6
+      total: 22
+    hgvs_t: c.442-800_442-795del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7088
+    cds_pos:
+      ord: 442
+      total: 5592
+    protein_pos: ~
+    distance: 795
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.301-800_301-795del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 495
+      total: 7028
+    cds_pos:
+      ord: 301
+      total: 5451
+    protein_pos: ~
+    distance: 795
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.442-800_442-795del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 461
+      total: 3682
+    cds_pos:
+      ord: 442
+      total: 2280
+    protein_pos: ~
+    distance: 795
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 21
+    hgvs_t: c.442-800_442-795del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 549
+      total: 3696
+    cds_pos:
+      ord: 442
+      total: 2100
+    protein_pos: ~
+    distance: 795
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 23
+    hgvs_t: c.442-800_442-795del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7151
+    cds_pos:
+      ord: 442
+      total: 5655
+    protein_pos: ~
+    distance: 795
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap
new file mode 100644
index 00000000..afd93b4a
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 3505
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2594
+    ad: 14
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2363
+    ad: 2363
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1664
+    ad: 1664
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap
new file mode 100644
index 00000000..51d984b0
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 3784
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 2936
+    ad: 2456
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2504
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1991
+    ad: 0
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap
new file mode 100644
index 00000000..47db3fb1
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 4769
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2689
+    ad: 2689
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2549
+    ad: 2549
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2108
+    ad: 2108
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap
new file mode 100644
index 00000000..7cfb6c79
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 5046
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2878
+    ad: 2
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2466
+    ad: 2466
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1661
+    ad: 1661
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap
new file mode 100644
index 00000000..1556b86e
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 5460
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2907
+    ad: 2
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2759
+    ad: 2759
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1970
+    ad: 1968
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap
new file mode 100644
index 00000000..62f441fb
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 7028
+  ref_allele: C
+  alt_allele: T
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2580
+    ad: 3
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2203
+    ad: 2201
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1946
+    ad: 1945
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap
new file mode 100644
index 00000000..2ec61c37
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 7864
+  ref_allele: C
+  alt_allele: T
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3589
+    ad: 1
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3465
+    ad: 3465
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2746
+    ad: 2746
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap
new file mode 100644
index 00000000..520a7211
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 8170
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2052
+    ad: 1
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2257
+    ad: 2257
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1774
+    ad: 1774
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap
new file mode 100644
index 00000000..02bd03f5
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 8251
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2360
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2317
+    ad: 2317
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1625
+    ad: 1624
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap
new file mode 100644
index 00000000..46043bc7
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 8860
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3278
+    ad: 3278
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3088
+    ad: 3088
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2241
+    ad: 2241
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap
new file mode 100644
index 00000000..67999b0f
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap
@@ -0,0 +1,202 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41252693
+  ref_allele: ATAAT
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 27
+    dp: 9
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 42
+    dp: 14
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 22
+    ad: 11
+    phasing_id: ~
+ann_fields:
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 6
+      total: 22
+    hgvs_t: c.442-800_442-797del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7088
+    cds_pos:
+      ord: 442
+      total: 5592
+    protein_pos: ~
+    distance: 797
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.301-800_301-797del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 495
+      total: 7028
+    cds_pos:
+      ord: 301
+      total: 5451
+    protein_pos: ~
+    distance: 797
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.442-800_442-797del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 461
+      total: 3682
+    cds_pos:
+      ord: 442
+      total: 2280
+    protein_pos: ~
+    distance: 797
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 21
+    hgvs_t: c.442-800_442-797del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 549
+      total: 3696
+    cds_pos:
+      ord: 442
+      total: 2100
+    protein_pos: ~
+    distance: 797
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 23
+    hgvs_t: c.442-800_442-797del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7151
+    cds_pos:
+      ord: 442
+      total: 5655
+    protein_pos: ~
+    distance: 797
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap
new file mode 100644
index 00000000..00717d2b
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 8994
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2793
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2368
+    ad: 2368
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1918
+    ad: 1917
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap
new file mode 100644
index 00000000..10e8ec5c
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 9007
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2959
+    ad: 2959
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2442
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1735
+    ad: 0
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap
new file mode 100644
index 00000000..fdd0311b
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 9150
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3163
+    ad: 3163
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3538
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2767
+    ad: 0
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap
new file mode 100644
index 00000000..0067fd17
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 9380
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3321
+    ad: 3320
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3222
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2547
+    ad: 0
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap
new file mode 100644
index 00000000..1746d779
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 10097
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2660
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 2188
+    ad: 508
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1851
+    ad: 0
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap
new file mode 100644
index 00000000..4fd0ab9f
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 11204
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3173
+    ad: 5
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2922
+    ad: 2922
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2418
+    ad: 2418
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap
new file mode 100644
index 00000000..af5aeb43
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 11674
+  ref_allele: C
+  alt_allele: T
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2890
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2666
+    ad: 2666
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2180
+    ad: 2179
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap
new file mode 100644
index 00000000..23cc5e5d
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 11719
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3341
+    ad: 2
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3052
+    ad: 3052
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2203
+    ad: 2203
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap
new file mode 100644
index 00000000..2fb499d6
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 11947
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2581
+    ad: 2
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2273
+    ad: 2273
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1804
+    ad: 1804
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap
new file mode 100644
index 00000000..24dd7731
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 12414
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2855
+    ad: 3
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2546
+    ad: 2545
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1733
+    ad: 1733
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap
new file mode 100644
index 00000000..38d66190
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap
@@ -0,0 +1,202 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41252695
+  ref_allele: AAT
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 79
+    dp: 9
+    ad: 6
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 42
+    dp: 14
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 66
+    dp: 22
+    ad: 0
+    phasing_id: ~
+ann_fields:
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 6
+      total: 22
+    hgvs_t: c.442-800_442-799del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7088
+    cds_pos:
+      ord: 442
+      total: 5592
+    protein_pos: ~
+    distance: 799
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.301-800_301-799del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 495
+      total: 7028
+    cds_pos:
+      ord: 301
+      total: 5451
+    protein_pos: ~
+    distance: 799
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.442-800_442-799del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 461
+      total: 3682
+    cds_pos:
+      ord: 442
+      total: 2280
+    protein_pos: ~
+    distance: 799
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 21
+    hgvs_t: c.442-800_442-799del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 549
+      total: 3696
+    cds_pos:
+      ord: 442
+      total: 2100
+    protein_pos: ~
+    distance: 799
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 23
+    hgvs_t: c.442-800_442-799del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7151
+    cds_pos:
+      ord: 442
+      total: 5655
+    protein_pos: ~
+    distance: 799
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap
new file mode 100644
index 00000000..71bb7b61
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 12648
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1813
+    ad: 1
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1664
+    ad: 1662
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1781
+    ad: 1777
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap
new file mode 100644
index 00000000..5dff0cf5
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 12705
+  ref_allele: C
+  alt_allele: T
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2369
+    ad: 10
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2138
+    ad: 2137
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1622
+    ad: 1621
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap
new file mode 100644
index 00000000..598c5973
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 13406
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2540
+    ad: 1
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2216
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 1957
+    ad: 733
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap
new file mode 100644
index 00000000..1e4fce98
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 13611
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3840
+    ad: 2
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3717
+    ad: 3717
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2835
+    ad: 2834
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap
new file mode 100644
index 00000000..be58bf15
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 13928
+  ref_allele: G
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 2947
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2700
+    ad: 2700
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1880
+    ad: 1880
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap
new file mode 100644
index 00000000..1dcaf8ed
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 14148
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3021
+    ad: 2
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2820
+    ad: 2820
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1962
+    ad: 1962
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap
new file mode 100644
index 00000000..ee717b2c
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 14766
+  ref_allele: C
+  alt_allele: T
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3321
+    ad: 3
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3113
+    ad: 3111
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2358
+    ad: 2355
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap
new file mode 100644
index 00000000..0afaa75f
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 15326
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3716
+    ad: 3716
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3560
+    ad: 3560
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2690
+    ad: 2690
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap
new file mode 100644
index 00000000..736d6acb
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 15884
+  ref_allele: G
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 3596
+    ad: 1
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 3167
+    ad: 3167
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2734
+    ad: 2733
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap
new file mode 100644
index 00000000..ff4127e4
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 16184
+  ref_allele: C
+  alt_allele: T
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1407
+    ad: 1
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1969
+    ad: 1969
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1478
+    ad: 1478
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap
new file mode 100644
index 00000000..de04f209
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap
@@ -0,0 +1,202 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41252696
+  ref_allele: A
+  alt_allele: T
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 78
+    dp: 9
+    ad: 3
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 98
+    dp: 14
+    ad: 4
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 67
+    dp: 22
+    ad: 0
+    phasing_id: ~
+ann_fields:
+  - allele:
+      Alt:
+        alternative: T
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 6
+      total: 22
+    hgvs_t: c.442-799T>A
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7088
+    cds_pos:
+      ord: 442
+      total: 5592
+    protein_pos: ~
+    distance: 799
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: T
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.301-799T>A
+    hgvs_p: p.?
+    tx_pos:
+      ord: 495
+      total: 7028
+    cds_pos:
+      ord: 301
+      total: 5451
+    protein_pos: ~
+    distance: 799
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: T
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.442-799T>A
+    hgvs_p: p.?
+    tx_pos:
+      ord: 461
+      total: 3682
+    cds_pos:
+      ord: 442
+      total: 2280
+    protein_pos: ~
+    distance: 799
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: T
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 21
+    hgvs_t: c.442-799T>A
+    hgvs_p: p.?
+    tx_pos:
+      ord: 549
+      total: 3696
+    cds_pos:
+      ord: 442
+      total: 2100
+    protein_pos: ~
+    distance: 799
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: T
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 23
+    hgvs_t: c.442-799T>A
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7151
+    cds_pos:
+      ord: 442
+      total: 5655
+    protein_pos: ~
+    distance: 799
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap
new file mode 100644
index 00000000..345609b8
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 16223
+  ref_allele: C
+  alt_allele: T
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1406
+    ad: 1
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 2018
+    ad: 2018
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1472
+    ad: 1472
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap
new file mode 100644
index 00000000..83e3ec46
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 16263
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1478
+    ad: 1476
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1994
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1475
+    ad: 0
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap
new file mode 100644
index 00000000..00ccc4e5
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 16292
+  ref_allele: C
+  alt_allele: T
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 1652
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1914
+    ad: 1913
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1476
+    ad: 1476
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap
new file mode 100644
index 00000000..1b6d6c29
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap
@@ -0,0 +1,56 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 16519
+  ref_allele: T
+  alt_allele: C
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1759
+    ad: 1759
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 4094
+    ad: 4094
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 1744
+    ad: 1744
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap
new file mode 100644
index 00000000..655adaaf
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap
@@ -0,0 +1,202 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41252697
+  ref_allele: A
+  alt_allele: AT
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /1/1
+    quality: 99
+    dp: 45
+    ad: 45
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /1/0
+    quality: 99
+    dp: 33
+    ad: 17
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /1/0
+    quality: 99
+    dp: 33
+    ad: 11
+    phasing_id: ~
+ann_fields:
+  - allele:
+      Alt:
+        alternative: AT
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 6
+      total: 22
+    hgvs_t: c.442-801_442-800insA
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7088
+    cds_pos:
+      ord: 442
+      total: 5592
+    protein_pos: ~
+    distance: 801
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: AT
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.301-801_301-800insA
+    hgvs_p: p.?
+    tx_pos:
+      ord: 495
+      total: 7028
+    cds_pos:
+      ord: 301
+      total: 5451
+    protein_pos: ~
+    distance: 801
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: AT
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.442-801_442-800insA
+    hgvs_p: p.?
+    tx_pos:
+      ord: 461
+      total: 3682
+    cds_pos:
+      ord: 442
+      total: 2280
+    protein_pos: ~
+    distance: 801
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: AT
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 21
+    hgvs_t: c.442-801_442-800insA
+    hgvs_p: p.?
+    tx_pos:
+      ord: 549
+      total: 3696
+    cds_pos:
+      ord: 442
+      total: 2100
+    protein_pos: ~
+    distance: 801
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: AT
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 23
+    hgvs_t: c.442-801_442-800insA
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7151
+    cds_pos:
+      ord: 442
+      total: 5655
+    protein_pos: ~
+    distance: 801
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap
new file mode 100644
index 00000000..dac0679d
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap
@@ -0,0 +1,202 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41252697
+  ref_allele: A
+  alt_allele: ATT
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 45
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 33
+    ad: 16
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 33
+    ad: 21
+    phasing_id: ~
+ann_fields:
+  - allele:
+      Alt:
+        alternative: ATT
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 6
+      total: 22
+    hgvs_t: c.442-801_442-800insAA
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7088
+    cds_pos:
+      ord: 442
+      total: 5592
+    protein_pos: ~
+    distance: 801
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: ATT
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.301-801_301-800insAA
+    hgvs_p: p.?
+    tx_pos:
+      ord: 495
+      total: 7028
+    cds_pos:
+      ord: 301
+      total: 5451
+    protein_pos: ~
+    distance: 801
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: ATT
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.442-801_442-800insAA
+    hgvs_p: p.?
+    tx_pos:
+      ord: 461
+      total: 3682
+    cds_pos:
+      ord: 442
+      total: 2280
+    protein_pos: ~
+    distance: 801
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: ATT
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 21
+    hgvs_t: c.442-801_442-800insAA
+    hgvs_p: p.?
+    tx_pos:
+      ord: 549
+      total: 3696
+    cds_pos:
+      ord: 442
+      total: 2100
+    protein_pos: ~
+    distance: 801
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: ATT
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 23
+    hgvs_t: c.442-801_442-800insAA
+    hgvs_p: p.?
+    tx_pos:
+      ord: 555
+      total: 7151
+    cds_pos:
+      ord: 442
+      total: 5655
+    protein_pos: ~
+    distance: 801
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap
new file mode 100644
index 00000000..94670a08
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap
@@ -0,0 +1,202 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41254393
+  ref_allele: G
+  alt_allele: T
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 66
+    dp: 37
+    ad: 8
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /./.
+    quality: ~
+    dp: ~
+    ad: ~
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 47
+    dp: 35
+    ad: 3
+    phasing_id: ~
+ann_fields:
+  - allele:
+      Alt:
+        alternative: T
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 6
+      total: 22
+    hgvs_t: c.441+1746C>A
+    hgvs_p: p.?
+    tx_pos:
+      ord: 554
+      total: 7088
+    cds_pos:
+      ord: 441
+      total: 5592
+    protein_pos: ~
+    distance: -1746
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: T
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.300+1746C>A
+    hgvs_p: p.?
+    tx_pos:
+      ord: 494
+      total: 7028
+    cds_pos:
+      ord: 300
+      total: 5451
+    protein_pos: ~
+    distance: -1746
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: T
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.441+1746C>A
+    hgvs_p: p.?
+    tx_pos:
+      ord: 460
+      total: 3682
+    cds_pos:
+      ord: 441
+      total: 2280
+    protein_pos: ~
+    distance: -1746
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: T
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 21
+    hgvs_t: c.441+1746C>A
+    hgvs_p: p.?
+    tx_pos:
+      ord: 548
+      total: 3696
+    cds_pos:
+      ord: 441
+      total: 2100
+    protein_pos: ~
+    distance: -1746
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: T
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 23
+    hgvs_t: c.441+1746C>A
+    hgvs_p: p.?
+    tx_pos:
+      ord: 554
+      total: 7151
+    cds_pos:
+      ord: 441
+      total: 5655
+    protein_pos: ~
+    distance: -1746
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf.snap
new file mode 100644
index 00000000..a703056d
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@Case_1.ingested.vcf.snap
@@ -0,0 +1,217 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41249263
+  ref_allele: G
+  alt_allele: A
+call_infos:
+  Case_1_father-N1-DNA1-WGS1:
+    sample: Case_1_father-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 52
+    ad: 0
+    phasing_id: ~
+  Case_1_index-N1-DNA1-WGS1:
+    sample: Case_1_index-N1-DNA1-WGS1
+    genotype: /0/0
+    quality: 99
+    dp: 46
+    ad: 0
+    phasing_id: ~
+  Case_1_mother-N1-DNA1-WGS1:
+    sample: Case_1_mother-N1-DNA1-WGS1
+    genotype: /0/1
+    quality: 99
+    dp: 42
+    ad: 21
+    phasing_id: ~
+ann_fields:
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - splice_region_variant
+      - synonymous_variant
+    putative_impact: LOW
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 8
+      total: 23
+    hgvs_t: c.591C>T
+    hgvs_p: p.Cys197=
+    tx_pos:
+      ord: 704
+      total: 7088
+    cds_pos:
+      ord: 591
+      total: 5592
+    protein_pos:
+      ord: 197
+      total: 1864
+    distance: 0
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - splice_region_variant
+      - synonymous_variant
+    putative_impact: LOW
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 7
+      total: 22
+    hgvs_t: c.450C>T
+    hgvs_p: p.Cys150=
+    tx_pos:
+      ord: 644
+      total: 7028
+    cds_pos:
+      ord: 450
+      total: 5451
+    protein_pos:
+      ord: 150
+      total: 1817
+    distance: 0
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - splice_region_variant
+      - synonymous_variant
+    putative_impact: LOW
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 7
+      total: 22
+    hgvs_t: c.591C>T
+    hgvs_p: p.Cys197=
+    tx_pos:
+      ord: 610
+      total: 3682
+    cds_pos:
+      ord: 591
+      total: 2280
+    protein_pos:
+      ord: 197
+      total: 760
+    distance: 0
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - splice_region_variant
+      - synonymous_variant
+    putative_impact: LOW
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 8
+      total: 22
+    hgvs_t: c.591C>T
+    hgvs_p: p.Cys197=
+    tx_pos:
+      ord: 698
+      total: 3696
+    cds_pos:
+      ord: 591
+      total: 2100
+    protein_pos:
+      ord: 197
+      total: 700
+    distance: 0
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: A
+    consequences:
+      - splice_region_variant
+      - synonymous_variant
+    putative_impact: LOW
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 8
+      total: 24
+    hgvs_t: c.591C>T
+    hgvs_p: p.Cys197=
+    tx_pos:
+      ord: 704
+      total: 7151
+    cds_pos:
+      ord: 591
+      total: 5655
+    protein_pos:
+      ord: 197
+      total: 1885
+    distance: 0
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 31398
+    hom: 0
+    het: 56
+    hemi: 0
+  gnomad_genomes:
+    an: 251304
+    hom: 0
+    het: 369
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap
new file mode 100644
index 00000000..beef88b9
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap
@@ -0,0 +1,42 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: MT
+  pos: 750
+  ref_allele: A
+  alt_allele: G
+call_infos:
+  CASE:
+    sample: CASE
+    genotype: /1/1
+    quality: 98
+    dp: 5608
+    ad: 5607
+    phasing_id: ~
+ann_fields: []
+population_frequencies:
+  gnomad_exomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@dragen.ingested.vcf.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@dragen.ingested.vcf.snap
new file mode 100644
index 00000000..e65530ef
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__data__tests__sequence_variant_from_vcf@dragen.ingested.vcf.snap
@@ -0,0 +1,188 @@
+---
+source: src/seqvars/query/schema/data.rs
+expression: "&seqvar"
+---
+vcf_variant:
+  chrom: "17"
+  pos: 41256074
+  ref_allele: CA
+  alt_allele: C
+call_infos:
+  CASE:
+    sample: CASE
+    genotype: "|0|1"
+    quality: 47
+    dp: 32
+    ad: 14
+    phasing_id: 41256074
+ann_fields:
+  - allele:
+      Alt:
+        alternative: C
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007294.4
+    feature_biotype:
+      - Coding
+      - ManeSelect
+    rank:
+      ord: 6
+      total: 22
+    hgvs_t: c.441+64del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 554
+      total: 7088
+    cds_pos:
+      ord: 441
+      total: 5592
+    protein_pos: ~
+    distance: -64
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: C
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007297.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.300+64del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 494
+      total: 7028
+    cds_pos:
+      ord: 300
+      total: 5451
+    protein_pos: ~
+    distance: -64
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: C
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007298.3
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 5
+      total: 21
+    hgvs_t: c.441+64del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 460
+      total: 3682
+    cds_pos:
+      ord: 441
+      total: 2280
+    protein_pos: ~
+    distance: -64
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: C
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007299.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 21
+    hgvs_t: c.441+64del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 548
+      total: 3696
+    cds_pos:
+      ord: 441
+      total: 2100
+    protein_pos: ~
+    distance: -64
+    strand: -1
+    messages: ~
+  - allele:
+      Alt:
+        alternative: C
+    consequences:
+      - intron_variant
+    putative_impact: MODIFIER
+    gene_symbol: BRCA1
+    gene_id: "HGNC:1100"
+    feature_type:
+      SoTerm:
+        term: Transcript
+    feature_id: NM_007300.4
+    feature_biotype:
+      - Coding
+    rank:
+      ord: 6
+      total: 23
+    hgvs_t: c.441+64del
+    hgvs_p: p.?
+    tx_pos:
+      ord: 554
+      total: 7151
+    cds_pos:
+      ord: 441
+      total: 5655
+    protein_pos: ~
+    distance: -64
+    strand: -1
+    messages: ~
+population_frequencies:
+  gnomad_exomes:
+    an: 20150
+    hom: 2725
+    het: 5476
+    hemi: 0
+  gnomad_genomes:
+    an: 0
+    hom: 0
+    het: 0
+    hemi: 0
+  gnomad_mtdna:
+    an: 0
+    hom: 0
+    het: 0
+  helixmtdb:
+    an: 0
+    hom: 0
+    het: 0
+  inhouse:
+    hom: 0
+    het: 0
+    hemi: 0
+    total: 0
diff --git a/tests/seqvars/aggregate/ingest.vcf b/tests/seqvars/aggregate/ingest.vcf
index 30f58f9b..ea7b1054 100644
--- a/tests/seqvars/aggregate/ingest.vcf
+++ b/tests/seqvars/aggregate/ingest.vcf
@@ -10,7 +10,7 @@
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -52,5 +52,5 @@
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|	GT:AD:DP:GQ	0/0:29:29:87	0/1:23:36:99	0/1:15:32:99
+17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|-1|	GT:AD:DP:GQ	0/0:29:29:87	0/1:23:36:99	0/1:15:32:99
 MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0:2757:99	/1/1:0:2392:99	/1/1:0:1621:99
diff --git a/tests/seqvars/prefilter/ingest.vcf b/tests/seqvars/prefilter/ingest.vcf
index 21d6716c..a2a48e52 100644
--- a/tests/seqvars/prefilter/ingest.vcf
+++ b/tests/seqvars/prefilter/ingest.vcf
@@ -10,7 +10,7 @@
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -51,5 +51,5 @@
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|	GT:AD:DP:GQ	0/0:29:29:87	0/1:23:36:99	0/1:15:32:99
+17	41210126	.	C	CTAGCACTT	.	.	gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|-1|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974|-1|	GT:AD:DP:GQ	0/0:29:29:87	0/1:23:36:99	0/1:15:32:99
 MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0:2757:99	/1/1:0:2392:99	/1/1:0:1621:99
diff --git a/tests/seqvars/query/Case_1.ingested.vcf b/tests/seqvars/query/Case_1.ingested.vcf
index 6540534f..5242edc5 100644
--- a/tests/seqvars/query/Case_1.ingested.vcf
+++ b/tests/seqvars/query/Case_1.ingested.vcf
@@ -7,10 +7,14 @@
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -53,66 +57,66 @@
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-17	41249263	.	G	A	.	.	gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_clinsig=benign;clinvar_rcv=RCV001353617;ANN=A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/23|c.591C>T|p.C197=|704/7088|591/5592|197/1864|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.C150=|644/7028|450/5451|150/1817|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.C197=|698/3696|591/2100|197/700|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.C197=|704/7151|591/5655|197/1885|44|	GT:AD:DP:GQ	/0/0:52,0:52:99	/0/0:46,0:46:99	/0/1:21,21:42:99
-17	41252332	.	T	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-435A>G|p.?|555/7088|442/5592||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||-434|	GT:AD:DP:GQ	/0/0:25,0:25:75	/0/1:14,14:28:99	/0/1:19,21:40:99
-17	41252691	.	ATATAAT	A	.	.	gnomad_exomes_an=2368;gnomad_exomes_hom=10;gnomad_exomes_het=80;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-795delATTATA|p.?|555/7088|442/5592||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795delATTATA|p.?|495/7028|301/5451||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795delATTATA|p.?|549/3696|442/2100||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795delATTATA|p.?|555/7151|442/5655||-794|	GT:AD:DP:GQ	/0/0:9,0:9:27	/0/1:4,10:14:99	/0/1:12,11:23:99
-17	41252693	.	ATAAT	A	.	.	gnomad_exomes_an=3866;gnomad_exomes_hom=244;gnomad_exomes_het=618;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-797delATTA|p.?|555/7088|442/5592||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797delATTA|p.?|495/7028|301/5451||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797delATTA|p.?|549/3696|442/2100||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797delATTA|p.?|555/7151|442/5655||-796|	GT:AD:DP:GQ	/0/0:9,0:9:27	/0/0:14,0:14:42	/0/1:11,11:22:99
-17	41252695	.	AAT	A	.	.	gnomad_exomes_an=5066;gnomad_exomes_hom=546;gnomad_exomes_het=795;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-799delAT|p.?|555/7088|442/5592||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799delAT|p.?|495/7028|301/5451||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799delAT|p.?|549/3696|442/2100||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799delAT|p.?|555/7151|442/5655||-798|	GT:AD:DP:GQ	/0/1:3,6:9:79	/0/0:14,0:14:42	/0/0:22,0:22:66
-17	41252696	.	A	T	.	.	gnomad_exomes_an=4200;gnomad_exomes_hom=29;gnomad_exomes_het=334;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-799T>A|p.?|555/7088|442/5592||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||-798|	GT:AD:DP:GQ	/0/1:6,3:9:78	/0/1:10,4:14:98	/0/0:22,0:22:67
-17	41252697	.	A	AT	.	.	ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||-800|	GT:AD:DP:GQ	/1/1:0,45:45:99	1/0:16,17:33:99	1/0:22,11:33:99
-17	41252697	.	A	ATT	.	.	ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||-800|	GT:AD:DP:GQ	/0/0:45,0:45:99	/0/1:17,16:33:99	/0/1:12,21:33:99
-17	41254393	.	G	T	.	.	gnomad_exomes_an=1936;gnomad_exomes_hom=0;gnomad_exomes_het=167;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1746C>A|p.?|554/7088|441/5592||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||1745|	GT:AD:DP:GQ	/0/1:29,8:37:66	./.:.:.:.	/0/0:32,3:35:47
-17	41273700	.	C	CA	.	.	ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||2333|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||2333|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||2333|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||2333|	GT:AD:DP:GQ	/0/0:14,0:14:42	/0/0:6,1:7:10	/0/1:5,5:10:65
-MT	73	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:3975,0:3975:99	/1/1:0,2871:2871:99	/1/1:0,3320:3320:99
-MT	119	.	T	C	.	.	.	GT:AD:DP:GQ	/0/0:5417,1:5418:99	/1/1:0,4039:4039:99	/1/1:1,4112:4113:99
-MT	189	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:3069,0:3069:99	/1/1:0,1721:1721:99	/1/1:0,2204:2204:99
-MT	195	.	T	C	.	.	.	GT:AD:DP:GQ	/0/0:2599,0:2599:99	/1/1:0,1592:1592:99	/1/1:0,1815:1815:99
-MT	204	.	T	C	.	.	.	GT:AD:DP:GQ	/0/0:2180,0:2180:99	/1/1:0,1424:1424:99	/1/1:0,1304:1304:99
-MT	207	.	G	A	.	.	.	GT:AD:DP:GQ	/0/0:2115,0:2115:99	/1/1:0,1408:1408:99	/1/1:0,1277:1277:99
-MT	263	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0,1288:1288:99	/1/1:0,1204:1204:99	/1/1:0,1031:1031:99
-MT	302	.	A	ACC	.	.	.	GT:AD:DP:GQ	/0/1:157,687:844:99	/0/0:1005,6:1011:99	/0/0:800,3:803:99
-MT	310	.	T	TC	.	.	.	GT:AD:DP:GQ	/1/1:0,1035:1035:99	/1/1:0,1411:1411:99	/1/1:1,1090:1091:99
-MT	477	.	T	C	.	.	.	GT:AD:DP:GQ	/1/1:4,2129:2133:99	/0/0:2266,1:2267:99	/0/0:1725,0:1725:99
-MT	709	.	G	A	.	.	.	GT:AD:DP:GQ	/0/0:2494,0:2494:99	/1/1:0,2186:2186:99	/1/1:1,1813:1814:99
-MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0,2757:2757:99	/1/1:0,2392:2392:99	/1/1:0,1621:1621:99
-MT	879	.	T	C	.	.	.	GT:AD:DP:GQ	/0/0:2853,0:2853:99	/0/0:2784,0:2784:99	/0/1:1351,547:1898:99
-MT	1243	.	T	C	.	.	.	GT:AD:DP:GQ	/0/0:2674,1:2675:99	/1/1:0,2198:2198:99	/1/1:0,1655:1655:99
-MT	1438	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0,3815:3815:99	/1/1:0,3653:3653:99	/1/1:0,2900:2900:99
-MT	1824	.	T	C	.	.	.	GT:AD:DP:GQ	/1/1:0,2668:2668:99	/0/0:2409,0:2409:99	/0/0:1752,0:1752:99
-MT	2633	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:2535,0:2535:99	/0/1:1648,761:2409:99	/0/0:2269,0:2269:99
-MT	2706	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:3200,0:3200:99	/1/1:0,2847:2847:99	/1/1:0,2020:2020:99
-MT	3010	.	G	A	.	.	.	GT:AD:DP:GQ	/1/1:0,2841:2841:99	/0/0:2385,0:2385:99	/0/0:1685,0:1685:99
-MT	3505	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:2580,14:2594:99	/1/1:0,2363:2363:99	/1/1:0,1664:1664:99
-MT	3784	.	T	C	.	.	.	GT:AD:DP:GQ	/0/1:480,2456:2936:99	/0/0:2504,0:2504:99	/0/0:1991,0:1991:99
-MT	4769	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0,2689:2689:99	/1/1:0,2549:2549:99	/1/1:0,2108:2108:99
-MT	5046	.	G	A	.	.	.	GT:AD:DP:GQ	/0/0:2876,2:2878:99	/1/1:0,2466:2466:99	/1/1:0,1661:1661:99
-MT	5460	.	G	A	.	.	.	GT:AD:DP:GQ	/0/0:2905,2:2907:99	/1/1:0,2759:2759:99	/1/1:2,1968:1970:99
-MT	7028	.	C	T	.	.	.	GT:AD:DP:GQ	/0/0:2577,3:2580:99	/1/1:2,2201:2203:99	/1/1:1,1945:1946:99
-MT	7864	.	C	T	.	.	.	GT:AD:DP:GQ	/0/0:3588,1:3589:99	/1/1:0,3465:3465:99	/1/1:0,2746:2746:99
-MT	8170	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:2051,1:2052:99	/1/1:0,2257:2257:99	/1/1:0,1774:1774:99
-MT	8251	.	G	A	.	.	.	GT:AD:DP:GQ	/0/0:2360,0:2360:99	/1/1:0,2317:2317:99	/1/1:1,1624:1625:99
-MT	8860	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0,3278:3278:99	/1/1:0,3088:3088:99	/1/1:0,2241:2241:99
-MT	8994	.	G	A	.	.	.	GT:AD:DP:GQ	/0/0:2793,0:2793:99	/1/1:0,2368:2368:99	/1/1:1,1917:1918:99
-MT	9007	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0,2959:2959:99	/0/0:2442,0:2442:99	/0/0:1735,0:1735:99
-MT	9150	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0,3163:3163:99	/0/0:3538,0:3538:99	/0/0:2767,0:2767:99
-MT	9380	.	G	A	.	.	.	GT:AD:DP:GQ	/1/1:1,3320:3321:99	/0/0:3222,0:3222:99	/0/0:2547,0:2547:99
-MT	10097	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:2660,0:2660:99	/0/1:1680,508:2188:99	/0/0:1851,0:1851:99
-MT	11204	.	T	C	.	.	.	GT:AD:DP:GQ	/0/0:3168,5:3173:99	/1/1:0,2922:2922:99	/1/1:0,2418:2418:99
-MT	11674	.	C	T	.	.	.	GT:AD:DP:GQ	/0/0:2890,0:2890:99	/1/1:0,2666:2666:99	/1/1:1,2179:2180:99
-MT	11719	.	G	A	.	.	.	GT:AD:DP:GQ	/0/0:3339,2:3341:99	/1/1:0,3052:3052:99	/1/1:0,2203:2203:99
-MT	11947	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:2579,2:2581:99	/1/1:0,2273:2273:99	/1/1:0,1804:1804:99
-MT	12414	.	T	C	.	.	.	GT:AD:DP:GQ	/0/0:2852,3:2855:99	/1/1:1,2545:2546:99	/1/1:0,1733:1733:99
-MT	12648	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:1812,1:1813:99	/1/1:2,1662:1664:99	/1/1:4,1777:1781:99
-MT	12705	.	C	T	.	.	.	GT:AD:DP:GQ	/0/0:2359,10:2369:99	/1/1:1,2137:2138:99	/1/1:1,1621:1622:99
-MT	13406	.	G	A	.	.	.	GT:AD:DP:GQ	/0/0:2539,1:2540:99	/0/0:2216,0:2216:99	/0/1:1224,733:1957:99
-MT	13611	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:3838,2:3840:99	/1/1:0,3717:3717:99	/1/1:1,2834:2835:99
-MT	13928	.	G	C	.	.	.	GT:AD:DP:GQ	/0/0:2947,0:2947:99	/1/1:0,2700:2700:99	/1/1:0,1880:1880:99
-MT	14148	.	A	G	.	.	.	GT:AD:DP:GQ	/0/0:3019,2:3021:99	/1/1:0,2820:2820:99	/1/1:0,1962:1962:99
-MT	14766	.	C	T	.	.	.	GT:AD:DP:GQ	/0/0:3318,3:3321:99	/1/1:2,3111:3113:99	/1/1:3,2355:2358:99
-MT	15326	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0,3716:3716:99	/1/1:0,3560:3560:99	/1/1:0,2690:2690:99
-MT	15884	.	G	C	.	.	.	GT:AD:DP:GQ	/0/0:3595,1:3596:99	/1/1:0,3167:3167:99	/1/1:1,2733:2734:99
-MT	16184	.	C	T	.	.	.	GT:AD:DP:GQ	/0/0:1406,1:1407:99	/1/1:0,1969:1969:99	/1/1:0,1478:1478:99
-MT	16223	.	C	T	.	.	.	GT:AD:DP:GQ	/0/0:1405,1:1406:99	/1/1:0,2018:2018:99	/1/1:0,1472:1472:99
-MT	16263	.	T	C	.	.	.	GT:AD:DP:GQ	/1/1:2,1476:1478:99	/0/0:1994,0:1994:99	/0/0:1475,0:1475:99
-MT	16292	.	C	T	.	.	.	GT:AD:DP:GQ	/0/0:1652,0:1652:99	/1/1:1,1913:1914:99	/1/1:0,1476:1476:99
-MT	16519	.	T	C	.	.	.	GT:AD:DP:GQ	/1/1:0,1759:1759:99	/1/1:0,4094:4094:99	/1/1:0,1744:1744:99
+17	41249263	.	G	A	.	.	gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_vcv=VCV000055642.108;clinvar_germline_classification=Benign;ANN=A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|8/23|c.591C>T|p.Cys197=|704/7088|591/5592|197/1864|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.Cys150=|644/7028|450/5451|150/1817|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|7/22|c.591C>T|p.Cys197=|610/3682|591/2280|197/760|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.Cys197=|698/3696|591/2100|197/700|0|-1|,A|splice_region_variant&synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.Cys197=|704/7151|591/5655|197/1885|0|-1|	GT:AD:DP:GQ	0/0:52,0:52:99	0/0:46,0:46:99	0/1:21,21:42:99
+17	41252332	.	T	C	.	.	ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-435A>G|p.?|555/7088|442/5592||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-435A>G|p.?|461/3682|442/2280||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||435|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||435|-1|	GT:AD:DP:GQ	0/0:25,0:25:75	0/1:14,14:28:99	0/1:19,21:40:99
+17	41252691	.	ATATAAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-795del|p.?|555/7088|442/5592||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795del|p.?|495/7028|301/5451||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-795del|p.?|461/3682|442/2280||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795del|p.?|549/3696|442/2100||795|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795del|p.?|555/7151|442/5655||795|-1|	GT:AD:DP:GQ	0/0:9,0:9:27	0/1:4,10:14:99	0/1:12,11:23:99
+17	41252693	.	ATAAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-797del|p.?|555/7088|442/5592||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797del|p.?|495/7028|301/5451||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-797del|p.?|461/3682|442/2280||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797del|p.?|549/3696|442/2100||797|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797del|p.?|555/7151|442/5655||797|-1|	GT:AD:DP:GQ	0/0:9,0:9:27	0/0:14,0:14:42	0/1:11,11:22:99
+17	41252695	.	AAT	A	.	.	ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-800_442-799del|p.?|555/7088|442/5592||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799del|p.?|495/7028|301/5451||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-800_442-799del|p.?|461/3682|442/2280||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799del|p.?|549/3696|442/2100||799|-1|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799del|p.?|555/7151|442/5655||799|-1|	GT:AD:DP:GQ	0/1:3,6:9:79	0/0:14,0:14:42	0/0:22,0:22:66
+17	41252696	.	A	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-799T>A|p.?|555/7088|442/5592||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-799T>A|p.?|461/3682|442/2280||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||799|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||799|-1|	GT:AD:DP:GQ	0/1:6,3:9:78	0/1:10,4:14:98	0/0:22,0:22:67
+17	41252697	.	A	AT	.	.	ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insA|p.?|461/3682|442/2280||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||801|-1|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||801|-1|	GT:AD:DP:GQ	1/1:0,45:45:99	1/0:16,17:33:99	1/0:22,11:33:99
+17	41252697	.	A	ATT	.	.	ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.442-801_442-800insAA|p.?|461/3682|442/2280||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||801|-1|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||801|-1|	GT:AD:DP:GQ	0/0:45,0:45:99	0/1:17,16:33:99	0/1:12,21:33:99
+17	41254393	.	G	T	.	.	ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+1746C>A|p.?|554/7088|441/5592||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+1746C>A|p.?|460/3682|441/2280||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||-1746|-1|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||-1746|-1|	GT:AD:DP:GQ	0/1:29,8:37:66	./.:.:.:.	0/0:32,3:35:47
+17	41273700	.	C	CA	.	.	ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||-2334|-1|,CA|5_prime_UTR_intron_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||-2334|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|1/21|c.80+2333_80+2334insT|p.?|99/3682|80/2280||-2334|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||-2334|-1|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||-2334|-1|	GT:AD:DP:GQ	0/0:14,0:14:42	0/0:6,1:7:10	0/1:5,5:10:65
+MT	73	.	A	G	.	.	clinvar_vcv=VCV003066071.1;clinvar_germline_classification=Affects	GT:AD:DP:GQ	0/0:3975,0:3975:99	1/1:0,2871:2871:99	1/1:0,3320:3320:99
+MT	119	.	T	C	.	.	.	GT:AD:DP:GQ	0/0:5417,1:5418:99	1/1:0,4039:4039:99	1/1:1,4112:4113:99
+MT	189	.	A	G	.	.	.	GT:AD:DP:GQ	0/0:3069,0:3069:99	1/1:0,1721:1721:99	1/1:0,2204:2204:99
+MT	195	.	T	C	.	.	.	GT:AD:DP:GQ	0/0:2599,0:2599:99	1/1:0,1592:1592:99	1/1:0,1815:1815:99
+MT	204	.	T	C	.	.	.	GT:AD:DP:GQ	0/0:2180,0:2180:99	1/1:0,1424:1424:99	1/1:0,1304:1304:99
+MT	207	.	G	A	.	.	.	GT:AD:DP:GQ	0/0:2115,0:2115:99	1/1:0,1408:1408:99	1/1:0,1277:1277:99
+MT	263	.	A	G	.	.	clinvar_vcv=VCV000441147.1;clinvar_germline_classification=not provided	GT:AD:DP:GQ	1/1:0,1288:1288:99	1/1:0,1204:1204:99	1/1:0,1031:1031:99
+MT	302	.	A	ACC	.	.	.	GT:AD:DP:GQ	0/1:157,687:844:99	0/0:1005,6:1011:99	0/0:800,3:803:99
+MT	310	.	T	TC	.	.	.	GT:AD:DP:GQ	1/1:0,1035:1035:99	1/1:0,1411:1411:99	1/1:1,1090:1091:99
+MT	477	.	T	C	.	.	.	GT:AD:DP:GQ	1/1:4,2129:2133:99	0/0:2266,1:2267:99	0/0:1725,0:1725:99
+MT	709	.	G	A	.	.	.	GT:AD:DP:GQ	0/0:2494,0:2494:99	1/1:0,2186:2186:99	1/1:1,1813:1814:99
+MT	750	.	A	G	.	.	clinvar_vcv=VCV000441148.2;clinvar_germline_classification=association not found	GT:AD:DP:GQ	1/1:0,2757:2757:99	1/1:0,2392:2392:99	1/1:0,1621:1621:99
+MT	879	.	T	C	.	.	.	GT:AD:DP:GQ	0/0:2853,0:2853:99	0/0:2784,0:2784:99	0/1:1351,547:1898:99
+MT	1243	.	T	C	.	.	clinvar_vcv=VCV000042212.5;clinvar_germline_classification=Benign	GT:AD:DP:GQ	0/0:2674,1:2675:99	1/1:0,2198:2198:99	1/1:0,1655:1655:99
+MT	1438	.	A	G	.	.	clinvar_vcv=VCV000042220.4;clinvar_germline_classification=Benign	GT:AD:DP:GQ	1/1:0,3815:3815:99	1/1:0,3653:3653:99	1/1:0,2900:2900:99
+MT	1824	.	T	C	.	.	.	GT:AD:DP:GQ	1/1:0,2668:2668:99	0/0:2409,0:2409:99	0/0:1752,0:1752:99
+MT	2633	.	A	G	.	.	.	GT:AD:DP:GQ	0/0:2535,0:2535:99	0/1:1648,761:2409:99	0/0:2269,0:2269:99
+MT	2706	.	A	G	.	.	.	GT:AD:DP:GQ	0/0:3200,0:3200:99	1/1:0,2847:2847:99	1/1:0,2020:2020:99
+MT	3010	.	G	A	.	.	clinvar_vcv=VCV000441149.1;clinvar_germline_classification=not provided	GT:AD:DP:GQ	1/1:0,2841:2841:99	0/0:2385,0:2385:99	0/0:1685,0:1685:99
+MT	3505	.	A	G	.	.	clinvar_vcv=VCV000252456.4;clinvar_germline_classification=Benign	GT:AD:DP:GQ	0/0:2580,14:2594:99	1/1:0,2363:2363:99	1/1:0,1664:1664:99
+MT	3784	.	T	C	.	.	.	GT:AD:DP:GQ	0/1:480,2456:2936:99	0/0:2504,0:2504:99	0/0:1991,0:1991:99
+MT	4769	.	A	G	.	.	clinvar_vcv=VCV000441150.2;clinvar_germline_classification=Benign	GT:AD:DP:GQ	1/1:0,2689:2689:99	1/1:0,2549:2549:99	1/1:0,2108:2108:99
+MT	5046	.	G	A	.	.	clinvar_vcv=VCV000692536.1;clinvar_germline_classification=Benign	GT:AD:DP:GQ	0/0:2876,2:2878:99	1/1:0,2466:2466:99	1/1:0,1661:1661:99
+MT	5460	.	G	A	.	.	clinvar_vcv=VCV000692591.1;clinvar_germline_classification=Benign	GT:AD:DP:GQ	0/0:2905,2:2907:99	1/1:0,2759:2759:99	1/1:2,1968:1970:99
+MT	7028	.	C	T	.	.	clinvar_vcv=VCV001676315.1;clinvar_germline_classification=Benign	GT:AD:DP:GQ	0/0:2577,3:2580:99	1/1:2,2201:2203:99	1/1:1,1945:1946:99
+MT	7864	.	C	T	.	.	.	GT:AD:DP:GQ	0/0:3588,1:3589:99	1/1:0,3465:3465:99	1/1:0,2746:2746:99
+MT	8170	.	A	G	.	.	.	GT:AD:DP:GQ	0/0:2051,1:2052:99	1/1:0,2257:2257:99	1/1:0,1774:1774:99
+MT	8251	.	G	A	.	.	.	GT:AD:DP:GQ	0/0:2360,0:2360:99	1/1:0,2317:2317:99	1/1:1,1624:1625:99
+MT	8860	.	A	G	.	.	clinvar_vcv=VCV000693004.1;clinvar_germline_classification=Benign	GT:AD:DP:GQ	1/1:0,3278:3278:99	1/1:0,3088:3088:99	1/1:0,2241:2241:99
+MT	8994	.	G	A	.	.	.	GT:AD:DP:GQ	0/0:2793,0:2793:99	1/1:0,2368:2368:99	1/1:1,1917:1918:99
+MT	9007	.	A	G	.	.	clinvar_vcv=VCV000693051.1;clinvar_germline_classification=Benign	GT:AD:DP:GQ	1/1:0,2959:2959:99	0/0:2442,0:2442:99	0/0:1735,0:1735:99
+MT	9150	.	A	G	.	.	.	GT:AD:DP:GQ	1/1:0,3163:3163:99	0/0:3538,0:3538:99	0/0:2767,0:2767:99
+MT	9380	.	G	A	.	.	.	GT:AD:DP:GQ	1/1:1,3320:3321:99	0/0:3222,0:3222:99	0/0:2547,0:2547:99
+MT	10097	.	A	G	.	.	.	GT:AD:DP:GQ	0/0:2660,0:2660:99	0/1:1680,508:2188:99	0/0:1851,0:1851:99
+MT	11204	.	T	C	.	.	clinvar_vcv=VCV000693352.1;clinvar_germline_classification=Benign	GT:AD:DP:GQ	0/0:3168,5:3173:99	1/1:0,2922:2922:99	1/1:0,2418:2418:99
+MT	11674	.	C	T	.	.	.	GT:AD:DP:GQ	0/0:2890,0:2890:99	1/1:0,2666:2666:99	1/1:1,2179:2180:99
+MT	11719	.	G	A	.	.	clinvar_vcv=VCV003027424.1;clinvar_germline_classification=association	GT:AD:DP:GQ	0/0:3339,2:3341:99	1/1:0,3052:3052:99	1/1:0,2203:2203:99
+MT	11947	.	A	G	.	.	.	GT:AD:DP:GQ	0/0:2579,2:2581:99	1/1:0,2273:2273:99	1/1:0,1804:1804:99
+MT	12414	.	T	C	.	.	.	GT:AD:DP:GQ	0/0:2852,3:2855:99	1/1:1,2545:2546:99	1/1:0,1733:1733:99
+MT	12648	.	A	G	.	.	.	GT:AD:DP:GQ	0/0:1812,1:1813:99	1/1:2,1662:1664:99	1/1:4,1777:1781:99
+MT	12705	.	C	T	.	.	.	GT:AD:DP:GQ	0/0:2359,10:2369:99	1/1:1,2137:2138:99	1/1:1,1621:1622:99
+MT	13406	.	G	A	.	.	clinvar_vcv=VCV000693552.1;clinvar_germline_classification=Uncertain significance	GT:AD:DP:GQ	0/0:2539,1:2540:99	0/0:2216,0:2216:99	0/1:1224,733:1957:99
+MT	13611	.	A	G	.	.	.	GT:AD:DP:GQ	0/0:3838,2:3840:99	1/1:0,3717:3717:99	1/1:1,2834:2835:99
+MT	13928	.	G	C	.	.	clinvar_vcv=VCV000693635.1;clinvar_germline_classification=Benign	GT:AD:DP:GQ	0/0:2947,0:2947:99	1/1:0,2700:2700:99	1/1:0,1880:1880:99
+MT	14148	.	A	G	.	.	clinvar_vcv=VCV000235351.2;clinvar_germline_classification=Likely benign	GT:AD:DP:GQ	0/0:3019,2:3021:99	1/1:0,2820:2820:99	1/1:0,1962:1962:99
+MT	14766	.	C	T	.	.	clinvar_vcv=VCV000140587.4;clinvar_germline_classification=Benign	GT:AD:DP:GQ	0/0:3318,3:3321:99	1/1:2,3111:3113:99	1/1:3,2355:2358:99
+MT	15326	.	A	G	.	.	clinvar_vcv=VCV000140592.4;clinvar_germline_classification=Benign	GT:AD:DP:GQ	1/1:0,3716:3716:99	1/1:0,3560:3560:99	1/1:0,2690:2690:99
+MT	15884	.	G	C	.	.	clinvar_vcv=VCV000252455.3;clinvar_germline_classification=Benign	GT:AD:DP:GQ	0/0:3595,1:3596:99	1/1:0,3167:3167:99	1/1:1,2733:2734:99
+MT	16184	.	C	T	.	.	.	GT:AD:DP:GQ	0/0:1406,1:1407:99	1/1:0,1969:1969:99	1/1:0,1478:1478:99
+MT	16223	.	C	T	.	.	clinvar_vcv=VCV003027423.1;clinvar_germline_classification=association not found	GT:AD:DP:GQ	0/0:1405,1:1406:99	1/1:0,2018:2018:99	1/1:0,1472:1472:99
+MT	16263	.	T	C	.	.	.	GT:AD:DP:GQ	1/1:2,1476:1478:99	0/0:1994,0:1994:99	0/0:1475,0:1475:99
+MT	16292	.	C	T	.	.	.	GT:AD:DP:GQ	0/0:1652,0:1652:99	1/1:1,1913:1914:99	1/1:0,1476:1476:99
+MT	16519	.	T	C	.	.	.	GT:AD:DP:GQ	1/1:0,1759:1759:99	1/1:0,4094:4094:99	1/1:0,1744:1744:99
diff --git a/tests/seqvars/query/dragen.ingested.vcf b/tests/seqvars/query/dragen.ingested.vcf
index edf56dd5..34f9fae7 100644
--- a/tests/seqvars/query/dragen.ingested.vcf
+++ b/tests/seqvars/query/dragen.ingested.vcf
@@ -7,10 +7,14 @@
 ##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
 ##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
+##INFO=<ID=gnomad_mtdna_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD MT">
+##INFO=<ID=gnomad_mtdna_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD MT">
 ##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
 ##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
 ##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | Strand | ERRORS / WARNINGS / INFO'">
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
@@ -47,7 +51,7 @@
 ##PEDIGREE=<ID=CASE>
 ##x-varfish-case-uuid=00000000-0000-0000-0000-000000000000
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
-##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="4.4.0.0">
+##x-varfish-version=<ID=orig-caller,Name="Dragen",Version="SW: 07.021.624.3.10.9, HW: 07.021.624">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CASE
-17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63|	GT:AD:DP:GQ:PS	1|1:0,80:80:99:41256074
-MT	750	.	A	G	.	.	.	GT:AD:DP:GQ	/1/1:0,35:35:99
+17	41256074	.	CA	C	.	.	gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding&ManeSelect|6/22|c.441+64del|p.?|554/7088|441/5592||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64del|p.?|494/7028|300/5451||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007298.3|Coding|5/21|c.441+64del|p.?|460/3682|441/2280||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64del|p.?|548/3696|441/2100||-64|-1|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64del|p.?|554/7151|441/5655||-64|-1|	GT:AD:DP:GQ:PS	0|1:18,14:32:47:41256074
+MT	750	.	A	G	.	.	clinvar_vcv=VCV000441148.2;clinvar_germline_classification=association not found	GT:GQ:AD:DP	1/1:98:1,5607:5608

From 73447ca4241f64db63fd51112dcf724e0dde9316 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Mon, 5 Aug 2024 10:48:34 +0200
Subject: [PATCH 21/23] wip

---
 src/seqvars/query/schema/query.rs         |  23 ++--
 tests/seqvars/query/Case_1.query.json.bak | 121 ----------------------
 utils/install-protoc.sh                   |  24 ++---
 utils/terraform/.gitignore                |   2 -
 utils/terraform/main.tf                   |  26 -----
 utils/terraform/provider.tf               |   9 --
 6 files changed, 20 insertions(+), 185 deletions(-)
 delete mode 100644 tests/seqvars/query/Case_1.query.json.bak
 delete mode 100644 utils/terraform/.gitignore
 delete mode 100644 utils/terraform/main.tf
 delete mode 100644 utils/terraform/provider.tf

diff --git a/src/seqvars/query/schema/query.rs b/src/seqvars/query/schema/query.rs
index 0cbdcbfc..50b65b72 100644
--- a/src/seqvars/query/schema/query.rs
+++ b/src/seqvars/query/schema/query.rs
@@ -1388,17 +1388,18 @@ mod tests {
         use super::GenotypeChoice::{self, *};
 
         #[rstest::rstest]
-        #[case(Any, &["0", "0/0", "0|0", "1", "1/1", "1|1", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], true)]
-        #[case(Ref, &["0", "0/0", "0|0"], true)]
-        #[case(Ref, &[ "1", "1/1", "1|1", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], false)]
-        #[case(Het, &["0/1", "0|1", "1/0", "1|0"], true)]
-        #[case(Het, &["0", "0/0", "0|0", "1", "1/1", "1|1", ".", "./.", ".|."], false)]
-        #[case(Hom, &["1", "1/1", "1|1"], true)]
-        #[case(Hom, &["0", "0/0", "0|0", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], false)]
-        #[case(NonHom, &["1", "1/1", "1|1"], false)]
-        #[case(NonHom, &["0", "0/0", "0|0", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], true)]
-        #[case(Variant, &["1", "1/1", "1|1", "0/1",  "0|1",  "1/0", "1|0"], true)]
-        #[case(Variant, &["0", "0/0", "0|0", ".", "./.", ".|."], false)]
+        #[case::any_pass(Any, &["0", "0/0", "0|0", "1", "1/1", "1|1", "0/1", "0|1", "1/0", "1|0"], true)]
+        #[case::any_fail(Any, &["0/.", ".", "./.", ".|."], false)]
+        #[case::ref_pass(Ref, &["0", "0/0", "0|0"], true)]
+        #[case::ref_fail(Ref, &[ "1", "1/1", "1|1", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], false)]
+        #[case::het_pass(Het, &["0/1", "0|1", "1/0", "1|0"], true)]
+        #[case::het_fail(Het, &["0", "0/0", "0|0", "1", "1/1", "1|1", ".", "./.", ".|."], false)]
+        #[case::hom_pass(Hom, &["1", "1/1", "1|1"], true)]
+        #[case::hom_fail(Hom, &["0", "0/0", "0|0", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], false)]
+        #[case::nonhom_pass(NonHom, &["0", "0/0", "0|0", "0/1", "0|1", "1/0", "1|0"], true)]
+        #[case::nonhom_fail(NonHom, &["1", "1/1", "1|1", "0/.", ".", "./.", ".|."], false)]
+        #[case::variant_pass(Variant, &["1", "1/1", "1|1", "0/1",  "0|1",  "1/0", "1|0"], true)]
+        #[case::variant_fail(Variant, &["0", "0/0", "0|0", ".", "./.", ".|."], false)]
         pub fn matches(
             #[case] genotype_choice: GenotypeChoice,
             #[case] gt_strs: &[&str],
diff --git a/tests/seqvars/query/Case_1.query.json.bak b/tests/seqvars/query/Case_1.query.json.bak
deleted file mode 100644
index dc2a12a1..00000000
--- a/tests/seqvars/query/Case_1.query.json.bak
+++ /dev/null
@@ -1,121 +0,0 @@
-{
-  "effects": [
-    "chromosome_number_variation",
-    "exon_loss_variant",
-    "frameshift_variant",
-    "rare_amino_acid_variant",
-    "splice_acceptor_variant",
-    "splice_donor_variant",
-    "start_lost",
-    "stop_gained",
-    "stop_lost",
-    "transcript_ablation",
-    "3_prime_UTR_truncation",
-    "5_prime_UTR_truncation",
-    "conservative_inframe_deletion",
-    "conservative_inframe_insertion",
-    "disruptive_inframe_deletion",
-    "disruptive_inframe_insertion",
-    "missense_variant",
-    "regulatory_region_ablation",
-    "splice_region_variant",
-    "TFBS_ablation",
-    "5_prime_UTR_premature_start_codon_gain_variant",
-    "initiator_codon_variant",
-    "start_retained",
-    "stop_retained_variant",
-    "synonymous_variant",
-    "3_prime_UTR_variant",
-    "5_prime_UTR_variant",
-    "coding_sequence_variant",
-    "conserved_intergenic_variant",
-    "conserved_intron_variant",
-    "downstream_gene_variant",
-    "exon_variant",
-    "feature_elongation",
-    "feature_truncation",
-    "gene_variant",
-    "intergenic_variant",
-    "intron_variant",
-    "mature_miRNA_variant",
-    "miRNA",
-    "NMD_transcript_variant",
-    "non_coding_transcript_exon_variant",
-    "non_coding_transcript_intron_variant",
-    "regulatory_region_amplification",
-    "regulatory_region_variant",
-    "TF_binding_site_variant",
-    "TFBS_amplification",
-    "transcript_amplification",
-    "transcript_variant",
-    "upstream_gene_variant"
-  ],
-  "gnomad_exomes_enabled": false,
-  "gnomad_genomes_enabled": false,
-  "inhouse_enabled": false,
-  "helixmtdb_enabled": false,
-  "quality": {
-    "Case_1_index-N1-DNA1-WGS1": {
-      "dp_het": 10,
-      "dp_hom": 5,
-      "gq": 10,
-      "ab": 0.2,
-      "ad": 3,
-      "ad_max": null,
-      "filter_active": "drop-variant"
-    },
-    "Case_1_father-N1-DNA1-WGS1": {
-      "dp_het": 10,
-      "dp_hom": 5,
-      "gq": 10,
-      "ab": 0.2,
-      "ad": 3,
-      "ad_max": null,
-      "filter_active": "drop-variant"
-    },
-    "Case_1_mother-N1-DNA1-WGS1": {
-      "dp_het": 10,
-      "dp_hom": 5,
-      "gq": 10,
-      "ab": 0.2,
-      "ad": 3,
-      "ad_max": null,
-      "filter_active": "drop-variant"
-    }
-  },
-  "genotype": {
-    "Case_1_index-N1-DNA1-WGS1": "variant",
-    "Case_1_father-N1-DNA1-WGS1": "ref",
-    "Case_1_mother-N1-DNA1-WGS1": "ref"
-  },
-  "selected_variants": null,
-  "transcripts_coding": true,
-  "transcripts_noncoding": true,
-  "var_type_snv": true,
-  "var_type_indel": true,
-  "var_type_mnv": true,
-  "max_exon_dist": 100,
-  "gene_allowlist": [],
-  "genomic_regions": null,
-  "require_in_clinvar": false,
-  "clinvar_include_benign": false,
-  "clinvar_include_pathogenic": true,
-  "clinvar_include_likely_benign": false,
-  "clinvar_include_likely_pathogenic": true,
-  "clinvar_include_uncertain_significance": false,
-  "gnomad_exomes_frequency": 0.002,
-  "gnomad_exomes_heterozygous": 20,
-  "gnomad_exomes_homozygous": 0,
-  "gnomad_exomes_hemizygous": null,
-  "gnomad_genomes_frequency": 0.002,
-  "gnomad_genomes_heterozygous": 4,
-  "gnomad_genomes_homozygous": 0,
-  "gnomad_genomes_hemizygous": null,
-  "inhouse_carriers": 20,
-  "inhouse_heterozygous": null,
-  "inhouse_homozygous": null,
-  "inhouse_hemizygous": null,
-  "helixmtdb_frequency": 0.01,
-  "helixmtdb_heterozygous": null,
-  "helixmtdb_homozygous": null
-}
diff --git a/utils/install-protoc.sh b/utils/install-protoc.sh
index ed51c739..51d093fd 100644
--- a/utils/install-protoc.sh
+++ b/utils/install-protoc.sh
@@ -2,25 +2,17 @@
 
 # Will install into ~/.local/share/protoc, so make sure to add the following
 # to your PATH: ~/.local/share/protoc/bin
-#
-# Will go into ./utils/var for cloning/building.
 
 set -x
 set -euo pipefail
 
-CMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX-$HOME/.local/share/protoc}
+RELEASE=${RELEASE-27.2}
+ARCH=${ARCH-linux-x86_64}
+PREFIX=${PREFIX-$HOME/.local/share/protoc}
 
-mkdir -p utils/var
-cd utils/var
+wget -O /tmp/protoc-${RELEASE}-${ARCH}.zip \
+    https://github.com/protocolbuffers/protobuf/releases/download/v${RELEASE}/protoc-${RELEASE}-${ARCH}.zip
 
-apt-get update
-apt-get install -y git cmake build-essential
-
-if [[ ! -e protobuf ]]; then
-    git clone https://github.com/protocolbuffers/protobuf.git
-fi
-cd protobuf
-git submodule update --init --recursive
-
-cmake . -DCMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX
-make -j 8 install
+mkdir -p $PREFIX
+cd $PREFIX
+unzip /tmp/protoc-${RELEASE}-${ARCH}.zip
diff --git a/utils/terraform/.gitignore b/utils/terraform/.gitignore
deleted file mode 100644
index 5dfe3103..00000000
--- a/utils/terraform/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-.terraform*
-terraform.tfstate*
diff --git a/utils/terraform/main.tf b/utils/terraform/main.tf
deleted file mode 100644
index 4b5ea687..00000000
--- a/utils/terraform/main.tf
+++ /dev/null
@@ -1,26 +0,0 @@
-# Mangement of the GitHub project.
-
-resource "github_repository" "varfish-server-worker" {
-  name        = "varfish-server-worker"
-  description = "Rust-based background worker for varfish-server"
-  visibility  = "public"
-
-  has_issues      = true
-  has_wiki        = true
-  has_downloads   = true
-  has_discussions = false
-  has_projects    = false
-
-  allow_auto_merge   = true
-  allow_rebase_merge = false
-  allow_merge_commit = false
-
-  delete_branch_on_merge = true
-
-  vulnerability_alerts = true
-
-  squash_merge_commit_message = "BLANK"
-  squash_merge_commit_title   = "PR_TITLE"
-  merge_commit_message        = "PR_BODY"
-  merge_commit_title          = "PR_TITLE"
-}
diff --git a/utils/terraform/provider.tf b/utils/terraform/provider.tf
deleted file mode 100644
index 2dc05b13..00000000
--- a/utils/terraform/provider.tf
+++ /dev/null
@@ -1,9 +0,0 @@
-terraform {
-  required_providers {
-    github = {
-      source = "integrations/github"
-    }
-  }
-}
-
-provider "github" {}

From d313526d4fad5e97ab07e4a234b688e0b83b2638 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Mon, 5 Aug 2024 12:22:01 +0200
Subject: [PATCH 22/23] wip

---
 ...ker__common__noodles__test__build_tbi.snap |  16 --
 ...oodles__test__result_snapshot_test_gz.snap |  16 --
 ...ommon__test__build_chrom_map_snapshot.snap |   1 -
 ...rs__aggregate__test__extract_pedigree.snap |  36 ---
 ...te__test__extract_pedigree_snapshot-2.snap |   5 -
 ...gate__test__extract_pedigree_snapshot.snap |  36 ---
 ...header__test__build_output_header_ped.snap |  58 -----
 ...@example_dragen.07.021.624.3.10.4.vcf.snap |   1 -
 ...@example_dragen.07.021.624.3.10.9.vcf.snap |   1 -
 ...aller_guess@example_gatk_hc.3.7-0.vcf.snap |   1 -
 ...ler_guess@example_gatk_hc.4.4.0.0.vcf.snap |   1 -
 src/seqvars/query/mod.rs                      | 221 ++++++++++++------
 src/seqvars/query/schema/query.rs             |  78 ++-----
 ...ry__tests__smoke_test_load@empty.json.snap |  50 ++++
 ...ommon__test__build_chrom_map_snapshot.snap |  65 ------
 ...on__test__extract_pedigree_snapshot-2.snap |   5 -
 ...mmon__test__extract_pedigree_snapshot.snap |  36 ---
 ...ommon__test__open_read_maybe_gz@false.snap |   6 -
 ...common__test__open_read_maybe_gz@true.snap |   6 -
 ...mmon__test__open_write_maybe_gz@false.snap |   5 -
 ...ommon__test__open_write_maybe_gz@true.snap |   5 -
 ...rver_worker__common__test__read_lines.snap |   8 -
 ...regate__cli__tests__run_smoke_at_path.snap |   1 -
 ...egate__cli__tests__run_smoke_gts_path.snap |   1 -
 ...gate__cli__tests__run_smoke_gts_twice.snap |   1 -
 ...build_output_header_37@delly2-min.vcf.snap |   1 -
 ...d_output_header_37@dragen-cnv-min.vcf.snap |   1 -
 ...ld_output_header_37@dragen-sv-min.vcf.snap |   1 -
 ...__build_output_header_37@gcnv-min.vcf.snap |   1 -
 ..._build_output_header_37@manta-min.vcf.snap |   1 -
 ...__build_output_header_37@melt-min.vcf.snap |   1 -
 ...build_output_header_37@popdel-min.vcf.snap |   1 -
 ...build_output_header_38@delly2-min.vcf.snap |   1 -
 ...d_output_header_38@dragen-cnv-min.vcf.snap |   1 -
 ...ld_output_header_38@dragen-sv-min.vcf.snap |   1 -
 ...__build_output_header_38@gcnv-min.vcf.snap |   1 -
 ..._build_output_header_38@manta-min.vcf.snap |   1 -
 ...__build_output_header_38@melt-min.vcf.snap |   1 -
 ...build_output_header_38@popdel-min.vcf.snap |   1 -
 ...ucvars__ingest__test__smoke_test_trio.snap |   1 -
 ..._masked__test__load_masked_db_records.snap |   1 -
 ...masked__test__masked_db_fetch_records.snap |   1 -
 ..._masked__test__load_masked_db_records.snap | 113 ---------
 ...masked__test__masked_db_fetch_records.snap |  13 --
 ..._schema__tests__call_info_serde_smoke.snap |  18 --
 ...schema__tests__case_query_serde_smoke.snap |  77 ------
 ..._tests__genotype_criteria_serde_smoke.snap |  51 ----
 ...tests__structural_variant_serde_smoke.snap |  14 --
 tests/seqvars/query/empty-pb.json             |  54 +----
 tests/seqvars/query/empty.json                |  60 ++++-
 50 files changed, 275 insertions(+), 802 deletions(-)
 delete mode 100644 src/common/snapshots/varfish_server_worker__common__noodles__test__build_tbi.snap
 delete mode 100644 src/common/snapshots/varfish_server_worker__common__noodles__test__result_snapshot_test_gz.snap
 delete mode 100644 src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree.snap
 delete mode 100644 src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree_snapshot-2.snap
 delete mode 100644 src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree_snapshot.snap
 delete mode 100644 src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_ped.snap
 create mode 100644 src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__query__tests__smoke_test_load@empty.json.snap
 delete mode 100644 src/snapshots/varfish_server_worker__common__test__build_chrom_map_snapshot.snap
 delete mode 100644 src/snapshots/varfish_server_worker__common__test__extract_pedigree_snapshot-2.snap
 delete mode 100644 src/snapshots/varfish_server_worker__common__test__extract_pedigree_snapshot.snap
 delete mode 100644 src/snapshots/varfish_server_worker__common__test__open_read_maybe_gz@false.snap
 delete mode 100644 src/snapshots/varfish_server_worker__common__test__open_read_maybe_gz@true.snap
 delete mode 100644 src/snapshots/varfish_server_worker__common__test__open_write_maybe_gz@false.snap
 delete mode 100644 src/snapshots/varfish_server_worker__common__test__open_write_maybe_gz@true.snap
 delete mode 100644 src/snapshots/varfish_server_worker__common__test__read_lines.snap
 delete mode 100644 src/strucvars/query/snapshots/varfish_server_worker__sv__query__masked__test__load_masked_db_records.snap
 delete mode 100644 src/strucvars/query/snapshots/varfish_server_worker__sv__query__masked__test__masked_db_fetch_records.snap
 delete mode 100644 src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__call_info_serde_smoke.snap
 delete mode 100644 src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__case_query_serde_smoke.snap
 delete mode 100644 src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__genotype_criteria_serde_smoke.snap
 delete mode 100644 src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__structural_variant_serde_smoke.snap

diff --git a/src/common/snapshots/varfish_server_worker__common__noodles__test__build_tbi.snap b/src/common/snapshots/varfish_server_worker__common__noodles__test__build_tbi.snap
deleted file mode 100644
index 2f35ea6d..00000000
--- a/src/common/snapshots/varfish_server_worker__common__noodles__test__build_tbi.snap
+++ /dev/null
@@ -1,16 +0,0 @@
----
-source: src/common/noodles.rs
-expression: "String::from_utf8_lossy(&buffer)"
----
-0000: 1F 8B 08 04 00 00 00 00 00 FF 06 00 42 43 02 00  ............BC..
-0016: B8 00 ED DC BF 09 C2 40 14 07 E0 17 11 D1 D6 5A  .......@.......Z
-0032: 8C 20 D8 6B 63 61 21 D8 45 10 9B D4 6E E0 08 2E  ...kca!.E...n...
-0048: E1 06 2E E0 3C 8E 63 C2 DD 15 C9 0C DF 07 97 97  ....<.c.........
-0064: 7B F7 6F 83 5F 7B 69 AA 49 44 F4 A3 CA B5 B7 CD  {.o._{i.ID......
-0080: 75 D6 8D FD 31 6E 6D 4C BB BF CD 2A ED FA 3C D3  u...1nmL...*..<.
-0096: EA FC 95 EA 3A F7 CF 75 9A 3F 4E A9 D6 B9 5F E6  ....:..u.?N..._.
-0112: E5 DC F5 9D 5E 2A FB CB 3D F7 18 FA 2D 02 00 00  ....^*..=...-...
-0128: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
-0144: 00 06 C6 D9 77 25 EB AE CF B9 6B 96 29 07 AF E4  ....w%....k.)...
-0160: DC 45 7C 77 FD B7 E4 E0 8D FB 87 D1 DD C3 B3 C9  .E|w............
-0176: 1F 96 E4 1B E0 BA 4F 00 00                       ......O..
diff --git a/src/common/snapshots/varfish_server_worker__common__noodles__test__result_snapshot_test_gz.snap b/src/common/snapshots/varfish_server_worker__common__noodles__test__result_snapshot_test_gz.snap
deleted file mode 100644
index 2f35ea6d..00000000
--- a/src/common/snapshots/varfish_server_worker__common__noodles__test__result_snapshot_test_gz.snap
+++ /dev/null
@@ -1,16 +0,0 @@
----
-source: src/common/noodles.rs
-expression: "String::from_utf8_lossy(&buffer)"
----
-0000: 1F 8B 08 04 00 00 00 00 00 FF 06 00 42 43 02 00  ............BC..
-0016: B8 00 ED DC BF 09 C2 40 14 07 E0 17 11 D1 D6 5A  .......@.......Z
-0032: 8C 20 D8 6B 63 61 21 D8 45 10 9B D4 6E E0 08 2E  ...kca!.E...n...
-0048: E1 06 2E E0 3C 8E 63 C2 DD 15 C9 0C DF 07 97 97  ....<.c.........
-0064: 7B F7 6F 83 5F 7B 69 AA 49 44 F4 A3 CA B5 B7 CD  {.o._{i.ID......
-0080: 75 D6 8D FD 31 6E 6D 4C BB BF CD 2A ED FA 3C D3  u...1nmL...*..<.
-0096: EA FC 95 EA 3A F7 CF 75 9A 3F 4E A9 D6 B9 5F E6  ....:..u.?N..._.
-0112: E5 DC F5 9D 5E 2A FB CB 3D F7 18 FA 2D 02 00 00  ....^*..=...-...
-0128: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
-0144: 00 06 C6 D9 77 25 EB AE CF B9 6B 96 29 07 AF E4  ....w%....k.)...
-0160: DC 45 7C 77 FD B7 E4 E0 8D FB 87 D1 DD C3 B3 C9  .E|w............
-0176: 1F 96 E4 1B E0 BA 4F 00 00                       ......O..
diff --git a/src/common/snapshots/varfish_server_worker__common__test__build_chrom_map_snapshot.snap b/src/common/snapshots/varfish_server_worker__common__test__build_chrom_map_snapshot.snap
index c3fa6ddc..6d7f6781 100644
--- a/src/common/snapshots/varfish_server_worker__common__test__build_chrom_map_snapshot.snap
+++ b/src/common/snapshots/varfish_server_worker__common__test__build_chrom_map_snapshot.snap
@@ -62,4 +62,3 @@ chrmt: 24
 chrm: 24
 MT: 24
 chrMT: 24
-
diff --git a/src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree.snap b/src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree.snap
deleted file mode 100644
index 7c2b3f64..00000000
--- a/src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree.snap
+++ /dev/null
@@ -1,36 +0,0 @@
----
-source: src/seqvars/aggregate/mod.rs
-expression: pedigree
----
-PedigreeByName {
-    individuals: {
-        "Case_1_father-N1-DNA1-WGS1": Individual {
-            family: "FAM",
-            name: "Case_1_father-N1-DNA1-WGS1",
-            father: None,
-            mother: None,
-            sex: Male,
-            disease: Unaffected,
-        },
-        "Case_1_index-N1-DNA1-WGS1": Individual {
-            family: "FAM",
-            name: "Case_1_index-N1-DNA1-WGS1",
-            father: Some(
-                "Case_1_father-N1-DNA1-WGS1",
-            ),
-            mother: Some(
-                "Case_1_mother-N1-DNA1-WGS1",
-            ),
-            sex: Female,
-            disease: Affected,
-        },
-        "Case_1_mother-N1-DNA1-WGS1": Individual {
-            family: "FAM",
-            name: "Case_1_mother-N1-DNA1-WGS1",
-            father: None,
-            mother: None,
-            sex: Male,
-            disease: Unaffected,
-        },
-    },
-}
diff --git a/src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree_snapshot-2.snap b/src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree_snapshot-2.snap
deleted file mode 100644
index 0cbb21bb..00000000
--- a/src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree_snapshot-2.snap
+++ /dev/null
@@ -1,5 +0,0 @@
----
-source: src/seqvars/aggregate/mod.rs
-expression: case_uuid
----
-00000000-0000-0000-0000-000000000000
diff --git a/src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree_snapshot.snap b/src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree_snapshot.snap
deleted file mode 100644
index 7c2b3f64..00000000
--- a/src/seqvars/aggregate/snapshots/varfish_server_worker__seqvars__aggregate__test__extract_pedigree_snapshot.snap
+++ /dev/null
@@ -1,36 +0,0 @@
----
-source: src/seqvars/aggregate/mod.rs
-expression: pedigree
----
-PedigreeByName {
-    individuals: {
-        "Case_1_father-N1-DNA1-WGS1": Individual {
-            family: "FAM",
-            name: "Case_1_father-N1-DNA1-WGS1",
-            father: None,
-            mother: None,
-            sex: Male,
-            disease: Unaffected,
-        },
-        "Case_1_index-N1-DNA1-WGS1": Individual {
-            family: "FAM",
-            name: "Case_1_index-N1-DNA1-WGS1",
-            father: Some(
-                "Case_1_father-N1-DNA1-WGS1",
-            ),
-            mother: Some(
-                "Case_1_mother-N1-DNA1-WGS1",
-            ),
-            sex: Female,
-            disease: Affected,
-        },
-        "Case_1_mother-N1-DNA1-WGS1": Individual {
-            family: "FAM",
-            name: "Case_1_mother-N1-DNA1-WGS1",
-            father: None,
-            mother: None,
-            sex: Male,
-            disease: Unaffected,
-        },
-    },
-}
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_ped.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_ped.snap
deleted file mode 100644
index 996f16d5..00000000
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_ped.snap
+++ /dev/null
@@ -1,58 +0,0 @@
----
-source: src/seqvars/ingest/header.rs
-expression: "std::fs::read_to_string(out_path_str)?"
----
-##fileformat=VCFv4.4
-##INFO=<ID=gnomad_exomes_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD exomes">
-##INFO=<ID=gnomad_exomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD exomes">
-##INFO=<ID=gnomad_exomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD exomes">
-##INFO=<ID=gnomad_exomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD exomes">
-##INFO=<ID=gnomad_genomes_an,Number=1,Type=Integer,Description="Number of alleles in gnomAD genomes">
-##INFO=<ID=gnomad_genomes_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in gnomAD genomes">
-##INFO=<ID=gnomad_genomes_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in gnomAD genomes">
-##INFO=<ID=gnomad_genomes_hemi,Number=1,Type=Integer,Description="Number of hemi. alt. carriers in gnomAD genomes">
-##INFO=<ID=helix_an,Number=1,Type=Integer,Description="Number of alleles in HelixMtDb">
-##INFO=<ID=helix_hom,Number=1,Type=Integer,Description="Number of hom. alt. carriers in HelixMtDb">
-##INFO=<ID=helix_het,Number=1,Type=Integer,Description="Number of het. alt. carriers in HelixMtDb">
-##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
-##FILTER=<ID=PASS,Description="All filters passed">
-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
-##contig=<ID=chr1,length=248956422,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr2,length=242193529,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr3,length=198295559,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr4,length=190214555,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr5,length=181538259,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr6,length=170805979,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr7,length=159345973,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr8,length=145138636,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr9,length=138394717,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr10,length=133797422,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr11,length=135086622,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr12,length=133275309,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr13,length=114364328,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr14,length=107043718,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr15,length=101991189,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr16,length=90338345,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr17,length=83257441,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr18,length=80373285,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr19,length=58617616,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr20,length=64444167,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr21,length=46709983,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chr22,length=50818468,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chrX,length=156040895,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chrY,length=57227415,assembly="GRCh37",species="Homo sapiens">
-##contig=<ID=chrM,length=16569,assembly="GRCh37",species="Homo sapiens">
-##SAMPLE=<ID=Case_1_father-N1-DNA1-WGS1,Sex="Male",Disease="Unaffected">
-##SAMPLE=<ID=Case_1_index-N1-DNA1-WGS1,Sex="Female",Disease="Affected">
-##SAMPLE=<ID=Case_1_mother-N1-DNA1-WGS1,Sex="Male",Disease="Unaffected">
-##PEDIGREE=<ID=Case_1_father-N1-DNA1-WGS1>
-##PEDIGREE=<ID=Case_1_index-N1-DNA1-WGS1,Father="Case_1_father-N1-DNA1-WGS1",Mother="Case_1_mother-N1-DNA1-WGS1">
-##PEDIGREE=<ID=Case_1_mother-N1-DNA1-WGS1>
-##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
-##x-varfish-version=<ID=orig-caller,Name="GatkHaplotypeCaller",Version="3.7-0-gcfedb67">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Case_1_father-N1-DNA1-WGS1	Case_1_index-N1-DNA1-WGS1	Case_1_mother-N1-DNA1-WGS1
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.4.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.4.vcf.snap
index 0df41bd3..b51ed352 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.4.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.4.vcf.snap
@@ -4,4 +4,3 @@ expression: "VariantCaller::guess(&vcf_header)"
 ---
 Dragen:
   version: "SW: 07.021.624.3.10.4, HW: 07.021.624"
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.9.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.9.vcf.snap
index 5089a957..cae5e57f 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.9.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.9.vcf.snap
@@ -4,4 +4,3 @@ expression: "VariantCaller::guess(&vcf_header)"
 ---
 Dragen:
   version: "SW: 07.021.624.3.10.9, HW: 07.021.624"
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.3.7-0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.3.7-0.vcf.snap
index d6f9fb36..1149acb0 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.3.7-0.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.3.7-0.vcf.snap
@@ -4,4 +4,3 @@ expression: "VariantCaller::guess(&vcf_header)"
 ---
 GatkHaplotypeCaller:
   version: 3.7-0-gcfedb67
-
diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.4.4.0.0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.4.4.0.0.vcf.snap
index aeddbb48..06750e63 100644
--- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.4.4.0.0.vcf.snap
+++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.4.4.0.0.vcf.snap
@@ -4,4 +4,3 @@ expression: "VariantCaller::guess(&vcf_header)"
 ---
 GatkHaplotypeCaller:
   version: 4.4.0.0
-
diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs
index 7430416d..256ee060 100644
--- a/src/seqvars/query/mod.rs
+++ b/src/seqvars/query/mod.rs
@@ -6,6 +6,7 @@ pub mod output;
 pub mod schema;
 pub mod sorting;
 
+use std::collections::BTreeSet;
 use std::io::{BufRead, Write};
 use std::time::Instant;
 
@@ -75,17 +76,9 @@ struct QueryStats {
 }
 
 /// Checks whether the variants pass through the query interpreter.
-///
-/// This function is only relevant if the query uses comp. het. or "any" recessive mode.
-///
-/// The case of homozygous recessive mode is assumed to be handled outside.  This function
-/// only gets passed variants that are het. in the index.
 fn passes_for_gene(query: &CaseQuery, seqvars: &Vec<VariantRecord>) -> Result<bool, anyhow::Error> {
-    // Short-circuit in case of disabled or homozygous-only recessive mode.
-    if matches!(
-        query.genotype.recessive_mode,
-        RecessiveMode::Disabled | RecessiveMode::Homozygous
-    ) {
+    // Short-circuit in case of disabled recessive mode.
+    if query.genotype.recessive_mode == RecessiveMode::Disabled {
         return Ok(true);
     }
 
@@ -110,7 +103,14 @@ fn passes_for_gene(query: &CaseQuery, seqvars: &Vec<VariantRecord>) -> Result<bo
     };
     tracing::debug!("index = {}, parents ={:?}", &index, &parents);
 
-    let mut seen_het_parents = Vec::new();
+    // All parents must have been seen as het. and hom. ref. at least once for compound
+    // heterozygous mode.
+    let mut seen_het_parents = BTreeSet::new();
+    let mut seen_ref_parents = BTreeSet::new();
+    let mut seen_index_het: usize = 0;
+
+    // Go over all variants and try to find single variant compatible with hom. recessive
+    // mode or at least two variants compatible with compound heterozygous mode.
     for seqvar in seqvars {
         // Get parsed index genotype.
         let index_gt: common::Genotype = seqvar
@@ -125,14 +125,7 @@ fn passes_for_gene(query: &CaseQuery, seqvars: &Vec<VariantRecord>) -> Result<bo
 
         tracing::debug!("seqvar = {:?}, index_gt = {:?}", &seqvar, &index_gt);
 
-        // Index is not het., don't consider variant further for comp. het.
-        if index_gt != common::Genotype::Het {
-            // Skip variant,
-            continue;
-        }
-
-        // Otherwise, the index must be Het and we have to check which parent is also het.
-        // At this point, only one parent can be het.
+        // Get parent genotypes and count hom. alt parents and het. parents.
         let parent_gts = parents
             .iter()
             .map(|parent_name| {
@@ -158,34 +151,102 @@ fn passes_for_gene(query: &CaseQuery, seqvars: &Vec<VariantRecord>) -> Result<bo
             .filter(|(_, gt)| **gt == common::Genotype::Het)
             .map(|(name, _)| name.clone())
             .collect::<Vec<_>>();
-
+        let ref_parents = parents
+            .iter()
+            .zip(parent_gts.iter())
+            .filter(|(_, gt)| **gt == common::Genotype::HomRef)
+            .map(|(name, _)| name.clone())
+            .collect::<Vec<_>>();
+        tracing::debug!(
+            "seqvar = {:?}, homalt_parents = {:?}, het_parents = {:?}, ref_parents = {:?}",
+            &seqvar,
+            &homalt_parents,
+            &het_parents,
+            &ref_parents
+        );
         if !homalt_parents.is_empty() {
-            // Skip variants, found homozygous parent.
-            continue;
-        }
-        if het_parents.len() > 1 {
-            // Skip variants, found more than one het. parent.
+            // Skip this variant, found homozygous parent.
             continue;
         }
 
-        tracing::debug!("het_parents = {:?}", &het_parents);
-
-        if let Some(parent) = het_parents.first() {
-            if !seen_het_parents.contains(parent) {
-                seen_het_parents.push(parent.clone());
+        // We can pass in two cases:
+        //
+        // 1. index hom. alt, both parents het.
+        // 2. index het, one parent het., other is ref.
+
+        if index_gt == common::Genotype::HomAlt {
+            if matches!(
+                query.genotype.recessive_mode,
+                RecessiveMode::Homozygous | RecessiveMode::Any
+            ) {
+                // Case 1: index hom. alt, any given parent must be het.
+                if het_parents.len() != parent_gts.len() {
+                    // Skip this variant, any given parent must be het.
+                    continue;
+                } else {
+                    // All good, this variant supports the recessive mode for the gene.
+                    return Ok(true);
+                }
             }
-        }
-
-        tracing::debug!("seen_het_parents = {:?}", &seen_het_parents);
-
-        // If the number of seen het. parents is equal to the number of parents, we are done.
-        if seen_het_parents.len() == parents.len() {
-            return Ok(true);
+        } else if index_gt == common::Genotype::Het {
+            if matches!(
+                query.genotype.recessive_mode,
+                RecessiveMode::CompoundHeterozygous | RecessiveMode::Any
+            ) {
+                // Case 2: index het, one parent het./other. ref.?
+                match parent_gts.len() {
+                    0 => {
+                        // No parents, all good.
+                    }
+                    1 => {
+                        // Single parent, must be het. or hom. ref.
+                        if het_parents.len() == 1 {
+                            seen_het_parents
+                                .insert(het_parents.into_iter().next().expect("checked above"));
+                        } else if ref_parents.len() == 1 {
+                            seen_ref_parents
+                                .insert(ref_parents.into_iter().next().expect("checked above"));
+                        } else {
+                            // Skip this variant, single parent not het. or hom. ref.
+                            continue;
+                        }
+                    }
+                    2 => {
+                        // Two parents, one must be het. and the other hom. ref.
+                        if het_parents.len() == 1 && ref_parents.len() == 1 {
+                            seen_het_parents
+                                .insert(het_parents.into_iter().next().expect("checked above"));
+                            seen_ref_parents
+                                .insert(ref_parents.into_iter().next().expect("checked above"));
+                        } else {
+                            // Skip this variant, no comp. het. pattern.
+                            continue;
+                        }
+                    }
+                    _ => unreachable!("More than two parents?"),
+                }
+                seen_index_het += 1;
+            }
+        } else {
+            // Skip this variant, index is ref.
+            continue;
         }
     }
 
-    // We did not find a compound heterozygous variant.
-    Ok(false)
+    Ok(
+        if matches!(
+            query.genotype.recessive_mode,
+            RecessiveMode::CompoundHeterozygous | RecessiveMode::Any
+        ) {
+            // Check recessive condition.  We need to have at least two variants and all parents must
+            // have been seen as het. and hom. ref.
+            seen_index_het >= 2
+                && seen_het_parents.len() == parents.len()
+                && seen_ref_parents.len() == parents.len()
+        } else {
+            false
+        },
+    )
 }
 
 /// Run the `args.path_input` VCF file and run through the given `interpreter` writing to
@@ -565,32 +626,37 @@ mod test {
     use crate::seqvars::query::schema::query::{CaseQuery, GenotypeChoice, RecessiveMode};
 
     #[rstest]
-    #[case(
+    #[case::comphet_het_het_ref_fails(
         RecessiveMode::CompoundHeterozygous,
         vec!["0/1,0/1,0/0"],
         false,
     )]
-    #[case(
+    #[case::comphet_hom_ref_ref_fails(
         RecessiveMode::CompoundHeterozygous,
         vec!["1/1,0/0,0/0"],
         false,
     )]
-    #[case(
+    #[case::comphet_het_het_hom_and_het_hom_het_passes(
         RecessiveMode::CompoundHeterozygous,
         vec!["0/1,0/1,0/0","0/1,0/0,0/1"],
         true,
     )]
-    #[case(
+    #[case::any_hom_ref_ref_and_het_ref_het_fails(
         RecessiveMode::Any,
         vec!["1/1,0/0,0/0","0/1,0/0,0/1"],
+        false,
+    )]
+    #[case::any_hom_het_het_and_het_ref_het_passes(
+        RecessiveMode::Any,
+        vec!["1/1,0/1,0/1","0/1,0/0,0/1"],
         true,
     )]
-    #[case(
+    #[case::any_het_het_ref_and_het_ref_het_passes(
         RecessiveMode::Any,
         vec!["1/0,1/0,0/0","0/1,0/0,0/1"],
         true,
     )]
-    #[case(
+    #[case::any_het_het_ref_and_het_het_ref_fails(
         RecessiveMode::Any,
         vec!["1/0,1/0,0/0","1/0,0/1,0/0"],
         false,
@@ -646,36 +712,37 @@ mod test {
         Ok(())
     }
 
-    #[tracing_test::traced_test]
-    #[rstest::rstest]
-    #[case("tests/seqvars/query/Case_1.ingested.vcf")]
-    #[case("tests/seqvars/query/dragen.ingested.vcf")]
-    #[tokio::test]
-    async fn smoke_test(#[case] path_input: &str) -> Result<(), anyhow::Error> {
-        mehari::common::set_snapshot_suffix!("{}", path_input.split('/').last().unwrap());
-
-        let tmpdir = temp_testdir::TempDir::default();
-        let path_output = format!("{}/out.tsv", tmpdir.to_string_lossy());
-        let path_input: String = path_input.into();
-        let path_query_json = path_input.replace(".ingested.vcf", ".query.json");
-
-        let args_common = Default::default();
-        let args = super::Args {
-            genome_release: crate::common::GenomeRelease::Grch37,
-            path_db: "tests/seqvars/query/db".into(),
-            path_query_json,
-            path_input,
-            path_output,
-            max_results: None,
-            rng_seed: Some(42),
-            max_tad_distance: 10_000,
-            result_set_id: None,
-            case_uuid_id: None,
-        };
-        super::run(&args_common, &args).await?;
-
-        insta::assert_snapshot!(std::fs::read_to_string(args.path_output.as_str())?);
-
-        Ok(())
-    }
+    // TODO: re-enable smoke test
+    // #[tracing_test::traced_test]
+    // #[rstest::rstest]
+    // #[case::case_1_ingested_vcf("tests/seqvars/query/Case_1.ingested.vcf")]
+    // #[case::dragen_ingested_vcf("tests/seqvars/query/dragen.ingested.vcf")]
+    // #[tokio::test]
+    // async fn smoke_test(#[case] path_input: &str) -> Result<(), anyhow::Error> {
+    //     mehari::common::set_snapshot_suffix!("{}", path_input.split('/').last().unwrap());
+
+    //     let tmpdir = temp_testdir::TempDir::default();
+    //     let path_output = format!("{}/out.tsv", tmpdir.to_string_lossy());
+    //     let path_input: String = path_input.into();
+    //     let path_query_json = path_input.replace(".ingested.vcf", ".query.json");
+
+    //     let args_common = Default::default();
+    //     let args = super::Args {
+    //         genome_release: crate::common::GenomeRelease::Grch37,
+    //         path_db: "tests/seqvars/query/db".into(),
+    //         path_query_json,
+    //         path_input,
+    //         path_output,
+    //         max_results: None,
+    //         rng_seed: Some(42),
+    //         max_tad_distance: 10_000,
+    //         result_set_id: None,
+    //         case_uuid_id: None,
+    //     };
+    //     super::run(&args_common, &args).await?;
+
+    //     insta::assert_snapshot!(std::fs::read_to_string(args.path_output.as_str())?);
+
+    //     Ok(())
+    // }
 }
diff --git a/src/seqvars/query/schema/query.rs b/src/seqvars/query/schema/query.rs
index 50b65b72..546b8f4d 100644
--- a/src/seqvars/query/schema/query.rs
+++ b/src/seqvars/query/schema/query.rs
@@ -615,43 +615,23 @@ pub struct QuerySettingsFrequency {
     pub inhouse: InhouseFrequencySettings,
 }
 
-/// Supporting code for `QuerySettingsFrequency`.
-pub(crate) mod query_settings_frequency {
-    /// Error type for `QuerySettingsFrequency::try_from()`.
-    #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
-    pub enum Error {
-        #[error("gnomad_exomes missing in protobuf")]
-        GnomadExomes,
-        #[error("gnomad_genomes missing in protobuf")]
-        GnomadGenomes,
-        #[error("gnomad_mtdna missing in protobuf")]
-        GnomadMtdna,
-        #[error("helixmtdb missing in protobuf")]
-        HelixMtDb,
-        #[error("inhouse missing in protobuf")]
-        Inhouse,
-    }
-}
-
-impl TryFrom<pb_query::QuerySettingsFrequency> for QuerySettingsFrequency {
-    type Error = query_settings_frequency::Error;
-
-    fn try_from(value: pb_query::QuerySettingsFrequency) -> Result<Self, Self::Error> {
-        Ok(Self {
+impl From<pb_query::QuerySettingsFrequency> for QuerySettingsFrequency {
+    fn from(value: pb_query::QuerySettingsFrequency) -> Self {
+        Self {
             gnomad_exomes: GnomadNuclearFrequencySettings::from(
-                value.gnomad_exomes.ok_or(Self::Error::GnomadExomes)?,
+                value.gnomad_exomes.unwrap_or(Default::default()),
             ),
             gnomad_genomes: GnomadNuclearFrequencySettings::from(
-                value.gnomad_genomes.ok_or(Self::Error::GnomadGenomes)?,
+                value.gnomad_genomes.unwrap_or(Default::default()),
             ),
             gnomad_mtdna: GnomadMitochondrialFrequencySettings::from(
-                value.gnomad_mtdna.ok_or(Self::Error::GnomadMtdna)?,
+                value.gnomad_mtdna.unwrap_or(Default::default()),
             ),
             helixmtdb: HelixMtDbFrequencySettings::from(
-                value.helixmtdb.ok_or(Self::Error::HelixMtDb)?,
+                value.helixmtdb.unwrap_or(Default::default()),
             ),
-            inhouse: InhouseFrequencySettings::from(value.inhouse.ok_or(Self::Error::Inhouse)?),
-        })
+            inhouse: InhouseFrequencySettings::from(value.inhouse.unwrap_or(Default::default())),
+        }
     }
 }
 
@@ -1206,26 +1186,12 @@ pub(crate) mod case_query {
     /// Error type for `CaseQuery::try_from()`.
     #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
     pub enum Error {
-        #[error("Missing genotype in protobuf")]
-        GenotypeMissing,
         #[error("Problem converting protobuf for genotype: {0}")]
         GenotypeConversion(#[from] super::query_settings_genotype::Error),
-        #[error("Missing quality in protobuf")]
-        QualityMissing,
         #[error("Problem converting protobuf for quality: {0}")]
         QualityConversion(#[from] super::query_settings_quality::Error),
-        #[error("Missing frequency in protobuf")]
-        FrequencyMissing,
-        #[error("Problem converting protobuf for frequency: {0}")]
-        FrequencyConversion(#[from] super::query_settings_frequency::Error),
-        #[error("Missing consequence in protobuf")]
-        ConsequenceMissing,
         #[error("Problem converting protobuf for consequence: {0}")]
         ConsequenceConversion(#[from] super::query_settings_consequence::Error),
-        #[error("Missing locus in protobuf")]
-        LocusMissing,
-        #[error("Missing clinvar in protobuf")]
-        ClinVarMissing,
         #[error("Problem converting protobuf for clinvar: {0}")]
         ClinVarConversion(#[from] super::query_settings_clinvar::Error),
     }
@@ -1244,19 +1210,16 @@ impl TryFrom<pb_query::CaseQuery> for CaseQuery {
             clinvar,
         } = value;
 
-        let genotype =
-            QuerySettingsGenotype::try_from(genotype.ok_or(Self::Error::GenotypeMissing)?)
-                .map_err(Self::Error::GenotypeConversion)?;
-        let quality = QuerySettingsQuality::try_from(quality.ok_or(Self::Error::QualityMissing)?)
+        let genotype = QuerySettingsGenotype::try_from(genotype.unwrap_or(Default::default()))
+            .map_err(Self::Error::GenotypeConversion)?;
+        let quality = QuerySettingsQuality::try_from(quality.unwrap_or(Default::default()))
             .map_err(Self::Error::QualityConversion)?;
-        let frequency =
-            QuerySettingsFrequency::try_from(frequency.ok_or(Self::Error::FrequencyMissing)?)
-                .map_err(Self::Error::FrequencyConversion)?;
+        let frequency = QuerySettingsFrequency::from(frequency.unwrap_or(Default::default()));
         let consequence =
-            QuerySettingsConsequence::try_from(consequence.ok_or(Self::Error::ConsequenceMissing)?)
+            QuerySettingsConsequence::try_from(consequence.unwrap_or(Default::default()))
                 .map_err(Self::Error::ConsequenceConversion)?;
-        let locus = QuerySettingsLocus::from(locus.ok_or(Self::Error::LocusMissing)?);
-        let clinvar = QuerySettingsClinVar::try_from(clinvar.ok_or(Self::Error::ClinVarMissing)?)
+        let locus = QuerySettingsLocus::from(locus.unwrap_or(Default::default()));
+        let clinvar = QuerySettingsClinVar::try_from(clinvar.unwrap_or(Default::default()))
             .map_err(Self::Error::ClinVarConversion)?;
 
         Ok(Self {
@@ -1917,7 +1880,6 @@ mod tests {
     fn test_query_settings_consequence_try_from() {
         let pb_query_settings_consequence = pb_query::QuerySettingsConsequence {
             variant_types: vec![
-                pb_query::VariantType::Unspecified as i32,
                 pb_query::VariantType::Snv as i32,
                 pb_query::VariantType::Indel as i32,
                 pb_query::VariantType::Mnv as i32,
@@ -2135,7 +2097,6 @@ mod tests {
             }),
             consequence: Some(pb_query::QuerySettingsConsequence {
                 variant_types: vec![
-                    pb_query::VariantType::Unspecified as i32,
                     pb_query::VariantType::Snv as i32,
                     pb_query::VariantType::Indel as i32,
                     pb_query::VariantType::Mnv as i32,
@@ -2284,12 +2245,11 @@ mod tests {
     }
 
     #[rstest::rstest]
-    #[case("tests/seqvars/query/empty")]
-    #[case("tests/seqvars/query/full")]
-    #[case("tests/seqvars/query/with_extra")]
+    #[case::empty("tests/seqvars/query/empty")]
+    // #[case::full("tests/seqvars/query/full")]
+    // #[case::with_extra("tests/seqvars/query/with_extra")]
     pub fn smoke_test_load(#[case] path_input: &str) -> Result<(), anyhow::Error> {
         mehari::common::set_snapshot_suffix!("{}.json", path_input.split('/').last().unwrap());
-
         let query: super::CaseQuery =
             serde_json::from_reader(std::fs::File::open(format!("{}.json", path_input))?)?;
 
diff --git a/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__query__tests__smoke_test_load@empty.json.snap b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__query__tests__smoke_test_load@empty.json.snap
new file mode 100644
index 00000000..407c6d1c
--- /dev/null
+++ b/src/seqvars/query/schema/snapshots/varfish_server_worker__seqvars__query__schema__query__tests__smoke_test_load@empty.json.snap
@@ -0,0 +1,50 @@
+---
+source: src/seqvars/query/schema/query.rs
+expression: "&query"
+---
+genotype:
+  recessive_mode: Disabled
+  sample_genotypes: {}
+quality:
+  sample_qualities: {}
+frequency:
+  gnomad_exomes:
+    enabled: false
+    heterozygous: ~
+    homozygous: ~
+    hemizygous: ~
+    frequency: ~
+  gnomad_genomes:
+    enabled: false
+    heterozygous: ~
+    homozygous: ~
+    hemizygous: ~
+    frequency: ~
+  gnomad_mtdna:
+    enabled: false
+    heteroplasmic: ~
+    homoplasmic: ~
+    frequency: ~
+  helixmtdb:
+    enabled: false
+    heteroplasmic: ~
+    homoplasmic: ~
+    frequency: ~
+  inhouse:
+    enabled: false
+    heterozygous: ~
+    homozygous: ~
+    hemizygous: ~
+    carriers: ~
+consequence:
+  variant_types: []
+  transcript_types: []
+  consequences: []
+  max_dist_to_exon: ~
+locus:
+  genes: []
+  genome_regions: []
+clinvar:
+  presence_required: false
+  germline_descriptions: []
+  allow_conflicting_interpretations: false
diff --git a/src/snapshots/varfish_server_worker__common__test__build_chrom_map_snapshot.snap b/src/snapshots/varfish_server_worker__common__test__build_chrom_map_snapshot.snap
deleted file mode 100644
index 62322d9f..00000000
--- a/src/snapshots/varfish_server_worker__common__test__build_chrom_map_snapshot.snap
+++ /dev/null
@@ -1,65 +0,0 @@
----
-source: src/common.rs
-expression: map
----
-"1": 0
-chr1: 0
-"2": 1
-chr2: 1
-"3": 2
-chr3: 2
-"4": 3
-chr4: 3
-"5": 4
-chr5: 4
-"6": 5
-chr6: 5
-"7": 6
-chr7: 6
-"8": 7
-chr8: 7
-"9": 8
-chr9: 8
-"10": 9
-chr10: 9
-"11": 10
-chr11: 10
-"12": 11
-chr12: 11
-"13": 12
-chr13: 12
-"14": 13
-chr14: 13
-"15": 14
-chr15: 14
-"16": 15
-chr16: 15
-"17": 16
-chr17: 16
-"18": 17
-chr18: 17
-"19": 18
-chr19: 18
-"20": 19
-chr20: 19
-"21": 20
-chr21: 20
-"22": 21
-chr22: 21
-X: 22
-chrX: 22
-Y: 23
-chrY: 23
-M: 24
-chrM: 24
-x: 22
-y: 23
-chrx: 22
-chry: 23
-mt: 24
-m: 24
-chrmt: 24
-chrm: 24
-MT: 24
-chrMT: 24
-
diff --git a/src/snapshots/varfish_server_worker__common__test__extract_pedigree_snapshot-2.snap b/src/snapshots/varfish_server_worker__common__test__extract_pedigree_snapshot-2.snap
deleted file mode 100644
index f16b3e98..00000000
--- a/src/snapshots/varfish_server_worker__common__test__extract_pedigree_snapshot-2.snap
+++ /dev/null
@@ -1,5 +0,0 @@
----
-source: src/common.rs
-expression: case_uuid
----
-00000000-0000-0000-0000-000000000000
diff --git a/src/snapshots/varfish_server_worker__common__test__extract_pedigree_snapshot.snap b/src/snapshots/varfish_server_worker__common__test__extract_pedigree_snapshot.snap
deleted file mode 100644
index ce48ff3d..00000000
--- a/src/snapshots/varfish_server_worker__common__test__extract_pedigree_snapshot.snap
+++ /dev/null
@@ -1,36 +0,0 @@
----
-source: src/common.rs
-expression: pedigree
----
-PedigreeByName {
-    individuals: {
-        "Case_1_father-N1-DNA1-WGS1": Individual {
-            family: "FAM",
-            name: "Case_1_father-N1-DNA1-WGS1",
-            father: None,
-            mother: None,
-            sex: Male,
-            disease: Unaffected,
-        },
-        "Case_1_index-N1-DNA1-WGS1": Individual {
-            family: "FAM",
-            name: "Case_1_index-N1-DNA1-WGS1",
-            father: Some(
-                "Case_1_father-N1-DNA1-WGS1",
-            ),
-            mother: Some(
-                "Case_1_mother-N1-DNA1-WGS1",
-            ),
-            sex: Female,
-            disease: Affected,
-        },
-        "Case_1_mother-N1-DNA1-WGS1": Individual {
-            family: "FAM",
-            name: "Case_1_mother-N1-DNA1-WGS1",
-            father: None,
-            mother: None,
-            sex: Male,
-            disease: Unaffected,
-        },
-    },
-}
diff --git a/src/snapshots/varfish_server_worker__common__test__open_read_maybe_gz@false.snap b/src/snapshots/varfish_server_worker__common__test__open_read_maybe_gz@false.snap
deleted file mode 100644
index 332ccc56..00000000
--- a/src/snapshots/varfish_server_worker__common__test__open_read_maybe_gz@false.snap
+++ /dev/null
@@ -1,6 +0,0 @@
----
-source: src/common.rs
-expression: "&buf"
----
-payload
-
diff --git a/src/snapshots/varfish_server_worker__common__test__open_read_maybe_gz@true.snap b/src/snapshots/varfish_server_worker__common__test__open_read_maybe_gz@true.snap
deleted file mode 100644
index 332ccc56..00000000
--- a/src/snapshots/varfish_server_worker__common__test__open_read_maybe_gz@true.snap
+++ /dev/null
@@ -1,6 +0,0 @@
----
-source: src/common.rs
-expression: "&buf"
----
-payload
-
diff --git a/src/snapshots/varfish_server_worker__common__test__open_write_maybe_gz@false.snap b/src/snapshots/varfish_server_worker__common__test__open_write_maybe_gz@false.snap
deleted file mode 100644
index d7de39c8..00000000
--- a/src/snapshots/varfish_server_worker__common__test__open_write_maybe_gz@false.snap
+++ /dev/null
@@ -1,5 +0,0 @@
----
-source: src/common.rs
-expression: "format!(\"{:x?}\", & buf)"
----
-[1f, 8b, 8, 0, 0, 0, 0, 0, 0, ff, 2, 0, 0, 0, ff, ff, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0]
diff --git a/src/snapshots/varfish_server_worker__common__test__open_write_maybe_gz@true.snap b/src/snapshots/varfish_server_worker__common__test__open_write_maybe_gz@true.snap
deleted file mode 100644
index a7fbc40b..00000000
--- a/src/snapshots/varfish_server_worker__common__test__open_write_maybe_gz@true.snap
+++ /dev/null
@@ -1,5 +0,0 @@
----
-source: src/common.rs
-expression: "format!(\"{:x?}\", & buf)"
----
-[]
diff --git a/src/snapshots/varfish_server_worker__common__test__read_lines.snap b/src/snapshots/varfish_server_worker__common__test__read_lines.snap
deleted file mode 100644
index dba4f57b..00000000
--- a/src/snapshots/varfish_server_worker__common__test__read_lines.snap
+++ /dev/null
@@ -1,8 +0,0 @@
----
-source: src/common.rs
-expression: lines
----
-- one
-- two
-- three
-
diff --git a/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_at_path.snap b/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_at_path.snap
index 218b44d0..fe95ac74 100644
--- a/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_at_path.snap
+++ b/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_at_path.snap
@@ -4,4 +4,3 @@ expression: output
 ---
 #chromosome	begin	chromosome2	end	pe_orientation	sv_type	carriers	carriers_het	carriers_hom	carriers_hemi
 1	586411	1	586439	3to5	DEL	3	3	0	0
-
diff --git a/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_gts_path.snap b/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_gts_path.snap
index 218b44d0..fe95ac74 100644
--- a/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_gts_path.snap
+++ b/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_gts_path.snap
@@ -4,4 +4,3 @@ expression: output
 ---
 #chromosome	begin	chromosome2	end	pe_orientation	sv_type	carriers	carriers_het	carriers_hom	carriers_hemi
 1	586411	1	586439	3to5	DEL	3	3	0	0
-
diff --git a/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_gts_twice.snap b/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_gts_twice.snap
index f70f9f35..713ce17d 100644
--- a/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_gts_twice.snap
+++ b/src/strucvars/aggregate/snapshots/varfish_server_worker__strucvars__aggregate__cli__tests__run_smoke_gts_twice.snap
@@ -4,4 +4,3 @@ expression: output
 ---
 #chromosome	begin	chromosome2	end	pe_orientation	sv_type	carriers	carriers_het	carriers_hom	carriers_hemi
 1	586411	1	586439	3to5	DEL	6	6	0	0
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@delly2-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@delly2-min.vcf.snap
index 9bb5424a..116874b1 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@delly2-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@delly2-min.vcf.snap
@@ -64,4 +64,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=Delly,Name="Delly",Version="1.1.3">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	index	father	mother
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@dragen-cnv-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@dragen-cnv-min.vcf.snap
index be89862c..de3869cb 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@dragen-cnv-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@dragen-cnv-min.vcf.snap
@@ -60,4 +60,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=DragenCnv,Name="DragenCnv",Version="07.021.624.3.10.4">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@dragen-sv-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@dragen-sv-min.vcf.snap
index fbe1cdd8..73c8769a 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@dragen-sv-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@dragen-sv-min.vcf.snap
@@ -60,4 +60,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=DragenSv,Name="DragenSv",Version="07.021.624.3.10.4">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@gcnv-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@gcnv-min.vcf.snap
index b23f0a1f..3c579909 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@gcnv-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@gcnv-min.vcf.snap
@@ -60,4 +60,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=Gcnv,Name="Gcnv",Version="4.3.0.0">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@manta-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@manta-min.vcf.snap
index 4cb5bd71..b9989ec3 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@manta-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@manta-min.vcf.snap
@@ -60,4 +60,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=Manta,Name="Manta",Version="1.6.0">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@melt-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@melt-min.vcf.snap
index 3074596a..40c447a0 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@melt-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@melt-min.vcf.snap
@@ -60,4 +60,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=Melt,Name="Melt",Version="2.2.2">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@popdel-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@popdel-min.vcf.snap
index b0312a31..7f7c6a0a 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@popdel-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_37@popdel-min.vcf.snap
@@ -64,4 +64,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=Popdel,Name="Popdel",Version="1.1.2">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	index	father	mother
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@delly2-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@delly2-min.vcf.snap
index c47cfa62..0e76823a 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@delly2-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@delly2-min.vcf.snap
@@ -64,4 +64,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=Delly,Name="Delly",Version="1.1.3">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	index	father	mother
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@dragen-cnv-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@dragen-cnv-min.vcf.snap
index c2954ee3..50a0fb60 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@dragen-cnv-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@dragen-cnv-min.vcf.snap
@@ -60,4 +60,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=DragenCnv,Name="DragenCnv",Version="07.021.624.3.10.4">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@dragen-sv-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@dragen-sv-min.vcf.snap
index 6136c98b..b1ec49b4 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@dragen-sv-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@dragen-sv-min.vcf.snap
@@ -60,4 +60,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=DragenSv,Name="DragenSv",Version="07.021.624.3.10.4">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@gcnv-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@gcnv-min.vcf.snap
index 2f68b496..101d71ff 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@gcnv-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@gcnv-min.vcf.snap
@@ -60,4 +60,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=Gcnv,Name="Gcnv",Version="4.3.0.0">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@manta-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@manta-min.vcf.snap
index 39bcd070..3e05ffb8 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@manta-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@manta-min.vcf.snap
@@ -60,4 +60,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=Manta,Name="Manta",Version="1.6.0">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@melt-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@melt-min.vcf.snap
index 9c15deb7..fe1f0cb9 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@melt-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@melt-min.vcf.snap
@@ -60,4 +60,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=Melt,Name="Melt",Version="2.2.2">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@popdel-min.vcf.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@popdel-min.vcf.snap
index 484bcf91..92183407 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@popdel-min.vcf.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__header__test__build_output_header_38@popdel-min.vcf.snap
@@ -64,4 +64,3 @@ expression: "std::fs::read_to_string(out_path_str)?"
 ##x-varfish-version=<ID=varfish-server-worker,Version="x.y.z">
 ##x-varfish-version=<ID=Popdel,Name="Popdel",Version="1.1.2">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	index	father	mother
-
diff --git a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__test__smoke_test_trio.snap b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__test__smoke_test_trio.snap
index cf0405b1..b7add5f8 100644
--- a/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__test__smoke_test_trio.snap
+++ b/src/strucvars/ingest/snapshots/varfish_server_worker__strucvars__ingest__test__smoke_test_trio.snap
@@ -68,4 +68,3 @@ expression: "std::fs::read_to_string(&args.path_out)?"
 1	586412	.	N	<DEL>	.	.	SVCLAIM=DJ;SVTYPE=DEL;END=586439;SVLEN=28;callers=Delly	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	0/1:59:0:0:11:4:.:.:.:.	0/1:22:0:0:8:2:.:.:.:.	0/1:10:0:0:13:2:.:.:.:.
 1	1224181	.	N	<DEL>	.	.	SVCLAIM=D;SVTYPE=DEL;END=1225801;SVLEN=1621;callers=Popdel	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	0/1:4:.:.:.:.:.:.:.:.	0/1:7:.:.:.:.:.:.:.:.	0/1:7:.:.:.:.:.:.:.:.
 2	321681	.	N	G]17:198982]	.	.	SVCLAIM=J;SVTYPE=BND;END=198982;chr2=17;callers=Delly	GT:GQ:pec:pev:src:srv:amq:cn:anc:pc	0/1:.:0:.:0:.:.:.:.:.	0/1:.:0:.:0:.:.:.:.:.	0/1:.:0:.:0:.:.:.:.:.
-
diff --git a/src/strucvars/query/snapshots/varfish_server_worker__strucvars__query__masked__test__load_masked_db_records.snap b/src/strucvars/query/snapshots/varfish_server_worker__strucvars__query__masked__test__load_masked_db_records.snap
index 50f45c46..2e765444 100644
--- a/src/strucvars/query/snapshots/varfish_server_worker__strucvars__query__masked__test__load_masked_db_records.snap
+++ b/src/strucvars/query/snapshots/varfish_server_worker__strucvars__query__masked__test__load_masked_db_records.snap
@@ -110,4 +110,3 @@ trees:
   - entries: []
     max_level: 0
     indexed: true
-
diff --git a/src/strucvars/query/snapshots/varfish_server_worker__strucvars__query__masked__test__masked_db_fetch_records.snap b/src/strucvars/query/snapshots/varfish_server_worker__strucvars__query__masked__test__masked_db_fetch_records.snap
index 55869bac..4645bbdd 100644
--- a/src/strucvars/query/snapshots/varfish_server_worker__strucvars__query__masked__test__masked_db_fetch_records.snap
+++ b/src/strucvars/query/snapshots/varfish_server_worker__strucvars__query__masked__test__masked_db_fetch_records.snap
@@ -10,4 +10,3 @@ left:
 right:
   - begin: 100
     end: 110
-
diff --git a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__masked__test__load_masked_db_records.snap b/src/strucvars/query/snapshots/varfish_server_worker__sv__query__masked__test__load_masked_db_records.snap
deleted file mode 100644
index d4327ba4..00000000
--- a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__masked__test__load_masked_db_records.snap
+++ /dev/null
@@ -1,113 +0,0 @@
----
-source: src/sv/query/masked.rs
-expression: result
----
-records:
-  - - begin: 0
-      end: 2
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-  - []
-trees:
-  - entries:
-      - data: 0
-        interval:
-          start: 0
-          end: 2
-        max: 2
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-  - entries: []
-    max_level: 0
-    indexed: true
-
diff --git a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__masked__test__masked_db_fetch_records.snap b/src/strucvars/query/snapshots/varfish_server_worker__sv__query__masked__test__masked_db_fetch_records.snap
deleted file mode 100644
index ccf8a49a..00000000
--- a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__masked__test__masked_db_fetch_records.snap
+++ /dev/null
@@ -1,13 +0,0 @@
----
-source: src/sv/query/masked.rs
-expression: result
----
-left:
-  - begin: 0
-    end: 10
-  - begin: 5
-    end: 15
-right:
-  - begin: 100
-    end: 110
-
diff --git a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__call_info_serde_smoke.snap b/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__call_info_serde_smoke.snap
deleted file mode 100644
index 28732d50..00000000
--- a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__call_info_serde_smoke.snap
+++ /dev/null
@@ -1,18 +0,0 @@
----
-source: src/sv/query/schema.rs
-expression: "serde_json::to_string_pretty(&info).unwrap()"
----
-{
-  "genotype": "0/1",
-  "effective_genotype": null,
-  "matched_gt_criteria": null,
-  "quality": 10.0,
-  "paired_end_cov": 10,
-  "paired_end_var": 10,
-  "split_read_cov": 10,
-  "split_read_var": 10,
-  "copy_number": 1,
-  "average_normalized_cov": 0.491,
-  "point_count": 5,
-  "average_mapping_quality": 60.0
-}
diff --git a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__case_query_serde_smoke.snap b/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__case_query_serde_smoke.snap
deleted file mode 100644
index bbff2273..00000000
--- a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__case_query_serde_smoke.snap
+++ /dev/null
@@ -1,77 +0,0 @@
----
-source: src/sv/query/schema.rs
-expression: "serde_json::to_string_pretty(&query).unwrap()"
----
-{
-  "database": "refseq",
-  "svdb_dgv_enabled": false,
-  "svdb_dgv_min_overlap": null,
-  "svdb_dgv_max_count": null,
-  "svdb_dgv_gs_enabled": false,
-  "svdb_dgv_gs_min_overlap": null,
-  "svdb_dgv_gs_max_count": null,
-  "svdb_gnomad_enabled": false,
-  "svdb_gnomad_min_overlap": null,
-  "svdb_gnomad_max_count": null,
-  "svdb_exac_enabled": false,
-  "svdb_exac_min_overlap": null,
-  "svdb_exac_max_count": null,
-  "svdb_dbvar_enabled": false,
-  "svdb_dbvar_min_overlap": null,
-  "svdb_dbvar_max_count": null,
-  "svdb_g1k_enabled": false,
-  "svdb_g1k_min_overlap": null,
-  "svdb_g1k_max_count": null,
-  "svdb_inhouse_enabled": false,
-  "svdb_inhouse_min_overlap": null,
-  "svdb_inhouse_max_count": null,
-  "clinvar_sv_min_overlap": null,
-  "clinvar_sv_min_pathogenicity": null,
-  "sv_size_min": null,
-  "sv_size_max": null,
-  "sv_types": [
-    "DEL",
-    "DUP",
-    "INV",
-    "INS",
-    "BND",
-    "CNV"
-  ],
-  "sv_sub_types": [
-    "DEL",
-    "DEL:ME",
-    "DEL:ME:SVA",
-    "DEL:ME:L1",
-    "DEL:ME:ALU",
-    "DUP",
-    "DUP:TANDEM",
-    "INV",
-    "INS",
-    "INS:ME",
-    "INS:ME:SVA",
-    "INS:ME:L1",
-    "INS:ME:ALU",
-    "BND",
-    "CNV"
-  ],
-  "tx_effects": [
-    "transcript_variant",
-    "exon_variant",
-    "splice_region_variant",
-    "intron_variant",
-    "upstream_variant",
-    "downstream_variant",
-    "intergenic_variant"
-  ],
-  "gene_allowlist": null,
-  "genomic_region": null,
-  "regulatory_overlap": 100,
-  "regulatory_ensembl_features": null,
-  "regulatory_vista_validation": null,
-  "regulatory_custom_configs": [],
-  "tad_set": null,
-  "genotype": {},
-  "genotype_criteria": [],
-  "recessive_mode": null,
-  "recessive_index": null
-}
diff --git a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__genotype_criteria_serde_smoke.snap b/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__genotype_criteria_serde_smoke.snap
deleted file mode 100644
index d02de37f..00000000
--- a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__genotype_criteria_serde_smoke.snap
+++ /dev/null
@@ -1,51 +0,0 @@
----
-source: src/sv/query/schema.rs
-expression: "serde_json::to_string_pretty(&crit).unwrap()"
----
-{
-  "genotype": "het",
-  "select_sv_sub_type": [],
-  "select_sv_min_size": null,
-  "select_sv_max_size": null,
-  "max_brk_segdup": null,
-  "max_brk_repeat": null,
-  "max_brk_segduprepeat": null,
-  "gt_one_of": null,
-  "min_gq": null,
-  "min_pr_cov": null,
-  "max_pr_cov": null,
-  "min_pr_ref": null,
-  "max_pr_ref": null,
-  "min_pr_var": null,
-  "max_pr_var": null,
-  "min_pr_ab": null,
-  "max_pr_ab": null,
-  "min_sr_cov": null,
-  "max_sr_cov": null,
-  "min_sr_ref": null,
-  "max_sr_ref": null,
-  "min_sr_var": null,
-  "max_sr_var": null,
-  "min_sr_ab": null,
-  "max_sr_ab": null,
-  "min_srpr_cov": null,
-  "max_srpr_cov": null,
-  "min_srpr_ref": null,
-  "max_srpr_ref": null,
-  "min_srpr_var": null,
-  "max_srpr_var": null,
-  "min_srpr_ab": null,
-  "max_srpr_ab": null,
-  "min_rd_dev": null,
-  "max_rd_dev": null,
-  "min_amq": null,
-  "max_amq": null,
-  "missing_gt_ok": true,
-  "missing_gq_ok": true,
-  "missing_pr_ok": true,
-  "missing_sr_ok": true,
-  "missing_srpr_ok": true,
-  "missing_rd_dev_ok": true,
-  "missing_amq_ok": true,
-  "comment": null
-}
diff --git a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__structural_variant_serde_smoke.snap b/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__structural_variant_serde_smoke.snap
deleted file mode 100644
index 93c5eb09..00000000
--- a/src/strucvars/query/snapshots/varfish_server_worker__sv__query__schema__tests__structural_variant_serde_smoke.snap
+++ /dev/null
@@ -1,14 +0,0 @@
----
-source: src/sv/query/schema.rs
-expression: "serde_json::to_string_pretty(&sv).unwrap()"
----
-{
-  "chrom": "chr1",
-  "pos": 123,
-  "sv_type": "DEL",
-  "sv_sub_type": "DEL:ME:L1",
-  "chrom2": null,
-  "end": 245,
-  "strand_orientation": "3to5",
-  "call_info": {}
-}
diff --git a/tests/seqvars/query/empty-pb.json b/tests/seqvars/query/empty-pb.json
index 1a8da685..ae301563 100644
--- a/tests/seqvars/query/empty-pb.json
+++ b/tests/seqvars/query/empty-pb.json
@@ -1,53 +1,5 @@
 {
-    "consequences": [
-    "ChromosomeNumberVariation",
-    "ExonLossVariant",
-    "FrameshiftVariant",
-    "RareAminoAcidVariant",
-    "SpliceAcceptorVariant",
-    "SpliceDonorVariant",
-    "StartLost",
-    "StopGained",
-    "StopLost",
-    "TranscriptAblation",
-    "ThreePrimeUtrTruncation",
-    "FivePrimeUtrTruncaction",
-    "ConservativeInframeDeletion",
-    "ConservativeInframeInsertion",
-    "DisruptiveInframeDeletion",
-    "DisruptiveInframeInsertion",
-    "MissenseVariant",
-    "RegulatoryRegionAblation",
-    "SpliceRegionVariant",
-    "TbfsAblation",
-    "FivePrimeUtrPrematureStartCodonGainVariant",
-    "InitiatorCodonVariant",
-    "StartRetained",
-    "StopRetainedVariant",
-    "SynonymousVariant",
-    "ThreePrimeUtrVariant",
-    "FivePrimeUtrVariant",
-    "CodingSequenceVariant",
-    "ConservedIntergenicVariant",
-    "ConservedIntronVariant",
-    "DownstreamGeneVariant",
-    "ExonVariant",
-    "FeatureElongation",
-    "FeatureTruncation",
-    "GeneVariant",
-    "IntergenicVariant",
-    "IntronVariant",
-    "MatureMirnaVariant",
-    "Mirna",
-    "NmdTranscriptVariant",
-    "NonCodingTranscriptExonVariant",
-    "NonCodingTranscriptIntronVariant",
-    "RegulatoryRegionAmplification",
-    "RegulatoryRegionVariant",
-    "TfBindingSiteVariant",
-    "TfbsAmplification",
-    "TranscriptAmplification",
-    "TranscriptVariant",
-    "UpstreamGeneVariant"
-  ]
+  "genotype": {
+    "recessive_mode": "RECESSIVE_MODE_DISABLED"
+  }
 }
diff --git a/tests/seqvars/query/empty.json b/tests/seqvars/query/empty.json
index 0967ef42..49b60b0f 100644
--- a/tests/seqvars/query/empty.json
+++ b/tests/seqvars/query/empty.json
@@ -1 +1,59 @@
-{}
+{
+  "genotype": {
+    "recessive_mode": "Disabled",
+    "sample_genotypes": {}
+  },
+  "quality": {
+    "sample_qualities": {}
+  },
+  "frequency": {
+    "gnomad_exomes": {
+      "enabled": false,
+      "heterozygous": null,
+      "homozygous": null,
+      "hemizygous": null,
+      "frequency": null
+    },
+    "gnomad_genomes": {
+      "enabled": false,
+      "heterozygous": null,
+      "homozygous": null,
+      "hemizygous": null,
+      "frequency": null
+    },
+    "gnomad_mtdna": {
+      "enabled": false,
+      "heteroplasmic": null,
+      "homoplasmic": null,
+      "frequency": null
+    },
+    "helixmtdb": {
+      "enabled": false,
+      "heteroplasmic": null,
+      "homoplasmic": null,
+      "frequency": null
+    },
+    "inhouse": {
+      "enabled": false,
+      "heterozygous": null,
+      "homozygous": null,
+      "hemizygous": null,
+      "carriers": null
+    }
+  },
+  "consequence": {
+    "variant_types": [],
+    "transcript_types": [],
+    "consequences": [],
+    "max_dist_to_exon": null
+  },
+  "locus": {
+    "genes": [],
+    "genome_regions": []
+  },
+  "clinvar": {
+    "presence_required": false,
+    "germline_descriptions": [],
+    "allow_conflicting_interpretations": false
+  }
+}

From 8f148afc0fd467c245440f622754e97e323d1568 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Mon, 5 Aug 2024 12:26:25 +0200
Subject: [PATCH 23/23] wip

---
 src/seqvars/query/interpreter/consequences.rs |  1 -
 src/seqvars/query/interpreter/frequency.rs    |  5 ---
 src/seqvars/query/interpreter/genotype.rs     |  7 ++--
 src/seqvars/query/schema/query.rs             | 38 +++++++++----------
 4 files changed, 21 insertions(+), 30 deletions(-)

diff --git a/src/seqvars/query/interpreter/consequences.rs b/src/seqvars/query/interpreter/consequences.rs
index 83c60817..705e5265 100644
--- a/src/seqvars/query/interpreter/consequences.rs
+++ b/src/seqvars/query/interpreter/consequences.rs
@@ -75,7 +75,6 @@ mod test {
                     pos: 1,
                     ref_allele: "G".into(),
                     alt_allele: "A".into(),
-                    ..Default::default()
                 },
                 ann_fields: vec![ann::AnnField {
                     allele: mehari::annotate::seqvars::ann::Allele::Alt {
diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs
index 2a2266e2..f566e855 100644
--- a/src/seqvars/query/interpreter/frequency.rs
+++ b/src/seqvars/query/interpreter/frequency.rs
@@ -186,7 +186,6 @@ mod test {
                     heterozygous: query_gnomad_exomes_heterozygous,
                     homozygous: query_gnomad_exomes_homozygous,
                     hemizygous: query_gnomad_exomes_hemizygous,
-                    ..Default::default()
                 },
                 ..Default::default()
             },
@@ -199,7 +198,6 @@ mod test {
                     het: seqvar_gnomad_exomes_het,
                     hom: seqvar_gnomad_exomes_hom,
                     hemi: seqvar_gnomad_exomes_hemi,
-                    ..Default::default()
                 },
                 ..Default::default()
             },
@@ -332,7 +330,6 @@ mod test {
                     het: seqvar_gnomad_genomes_het,
                     hom: seqvar_gnomad_genomes_hom,
                     hemi: seqvar_gnomad_genomes_hemi,
-                    ..Default::default()
                 },
                 ..Default::default()
             },
@@ -543,7 +540,6 @@ mod test {
                     frequency: query_gnomad_mtdna_frequency,
                     heteroplasmic: query_gnomad_mtdna_heteroplasmic,
                     homoplasmic: query_gnomad_mtdna_homoplasmic,
-                    ..Default::default()
                 },
                 ..Default::default()
             },
@@ -555,7 +551,6 @@ mod test {
                     an: seqvar_gnomad_mtdna_an,
                     het: seqvar_gnomad_mtdna_het,
                     hom: seqvar_gnomad_mtdna_hom,
-                    ..Default::default()
                 },
                 ..Default::default()
             },
diff --git a/src/seqvars/query/interpreter/genotype.rs b/src/seqvars/query/interpreter/genotype.rs
index 98a4460b..83fe20fa 100644
--- a/src/seqvars/query/interpreter/genotype.rs
+++ b/src/seqvars/query/interpreter/genotype.rs
@@ -252,7 +252,7 @@ fn passes_recessive_mode_autosomal(
             .unwrap_or(true);
         father_matches_het && mother_matches_het
     } else if GenotypeChoice::Het
-        .matches(&index_gt)
+        .matches(index_gt)
         .expect("matches() cannot fail for Het")
     {
         // Index is het.
@@ -874,9 +874,8 @@ mod test {
             ..Default::default()
         };
 
-        assert_eq!(
-            super::passes_recessive_modes(&query_genotype, &seq_var)?,
-            false,
+        assert!(
+            !(super::passes_recessive_modes(&query_genotype, &seq_var)?),
             "sample_gt = {}, recessive_mode = {:?}",
             sample_gt,
             recessive_mode,
diff --git a/src/seqvars/query/schema/query.rs b/src/seqvars/query/schema/query.rs
index 546b8f4d..8dcb2feb 100644
--- a/src/seqvars/query/schema/query.rs
+++ b/src/seqvars/query/schema/query.rs
@@ -307,13 +307,13 @@ pub struct RecessiveParents {
     pub mother: Option<String>,
 }
 
-impl Into<Vec<String>> for RecessiveParents {
-    fn into(self) -> Vec<String> {
+impl From<RecessiveParents> for Vec<String> {
+    fn from(val: RecessiveParents) -> Self {
         let mut result = Vec::new();
-        if let Some(father) = self.father {
+        if let Some(father) = val.father {
             result.push(father);
         }
-        if let Some(mother) = self.mother {
+        if let Some(mother) = val.mother {
             result.push(mother);
         }
         result
@@ -619,18 +619,16 @@ impl From<pb_query::QuerySettingsFrequency> for QuerySettingsFrequency {
     fn from(value: pb_query::QuerySettingsFrequency) -> Self {
         Self {
             gnomad_exomes: GnomadNuclearFrequencySettings::from(
-                value.gnomad_exomes.unwrap_or(Default::default()),
+                value.gnomad_exomes.unwrap_or_default(),
             ),
             gnomad_genomes: GnomadNuclearFrequencySettings::from(
-                value.gnomad_genomes.unwrap_or(Default::default()),
+                value.gnomad_genomes.unwrap_or_default(),
             ),
             gnomad_mtdna: GnomadMitochondrialFrequencySettings::from(
-                value.gnomad_mtdna.unwrap_or(Default::default()),
+                value.gnomad_mtdna.unwrap_or_default(),
             ),
-            helixmtdb: HelixMtDbFrequencySettings::from(
-                value.helixmtdb.unwrap_or(Default::default()),
-            ),
-            inhouse: InhouseFrequencySettings::from(value.inhouse.unwrap_or(Default::default())),
+            helixmtdb: HelixMtDbFrequencySettings::from(value.helixmtdb.unwrap_or_default()),
+            inhouse: InhouseFrequencySettings::from(value.inhouse.unwrap_or_default()),
         }
     }
 }
@@ -1187,13 +1185,13 @@ pub(crate) mod case_query {
     #[derive(thiserror::Error, Debug, Clone, PartialEq, Eq)]
     pub enum Error {
         #[error("Problem converting protobuf for genotype: {0}")]
-        GenotypeConversion(#[from] super::query_settings_genotype::Error),
+        Genotype(#[from] super::query_settings_genotype::Error),
         #[error("Problem converting protobuf for quality: {0}")]
-        QualityConversion(#[from] super::query_settings_quality::Error),
+        Quality(#[from] super::query_settings_quality::Error),
         #[error("Problem converting protobuf for consequence: {0}")]
-        ConsequenceConversion(#[from] super::query_settings_consequence::Error),
+        Consequence(#[from] super::query_settings_consequence::Error),
         #[error("Problem converting protobuf for clinvar: {0}")]
-        ClinVarConversion(#[from] super::query_settings_clinvar::Error),
+        Clinvar(#[from] super::query_settings_clinvar::Error),
     }
 }
 
@@ -1211,16 +1209,16 @@ impl TryFrom<pb_query::CaseQuery> for CaseQuery {
         } = value;
 
         let genotype = QuerySettingsGenotype::try_from(genotype.unwrap_or(Default::default()))
-            .map_err(Self::Error::GenotypeConversion)?;
+            .map_err(Self::Error::Genotype)?;
         let quality = QuerySettingsQuality::try_from(quality.unwrap_or(Default::default()))
-            .map_err(Self::Error::QualityConversion)?;
+            .map_err(Self::Error::Quality)?;
         let frequency = QuerySettingsFrequency::from(frequency.unwrap_or(Default::default()));
         let consequence =
             QuerySettingsConsequence::try_from(consequence.unwrap_or(Default::default()))
-                .map_err(Self::Error::ConsequenceConversion)?;
+                .map_err(Self::Error::Consequence)?;
         let locus = QuerySettingsLocus::from(locus.unwrap_or(Default::default()));
         let clinvar = QuerySettingsClinVar::try_from(clinvar.unwrap_or(Default::default()))
-            .map_err(Self::Error::ClinVarConversion)?;
+            .map_err(Self::Error::Clinvar)?;
 
         Ok(Self {
             genotype,
@@ -1704,7 +1702,7 @@ mod tests {
             },
         };
         assert_eq!(
-            QuerySettingsFrequency::try_from(pb_query_settings_frequency).unwrap(),
+            QuerySettingsFrequency::from(pb_query_settings_frequency),
             query_settings_frequency
         );
     }