From ad4d1b16c652180c458cc30989be67b5bfce0ee0 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Fri, 20 Oct 2023 18:26:36 +0200 Subject: [PATCH 1/5] fix: make distance to next exon correct (#222) --- src/annotate/seqvars/csq.rs | 22 ++++++++++++++----- ..._test__annotate_snv_brca1_one_variant.snap | 2 +- 2 files changed, 17 insertions(+), 7 deletions(-) diff --git a/src/annotate/seqvars/csq.rs b/src/annotate/seqvars/csq.rs index 7b2f7282..5627e65a 100644 --- a/src/annotate/seqvars/csq.rs +++ b/src/annotate/seqvars/csq.rs @@ -715,8 +715,18 @@ mod test { is_sync::(); } - #[test] - fn annotate_snv_brca1_one_variant() -> Result<(), anyhow::Error> { + #[rstest::rstest] + #[case("17:41197701:G:C")] + #[case("17:41197695:G:C")] + #[case("17:41197694:G:C")] + #[case("17:41197694:G:C")] + #[case("17:41197693:G:C")] + #[case("17:41197692:G:C")] + fn annotate_snv_brca1_one_variant(#[case] spdi: &str) -> Result<(), anyhow::Error> { + crate::common::set_snapshot_suffix!("{}", spdi.replace(":", "-")); + + let spdi = spdi.split(":").into_iter().map(|s| s.to_string()).collect::>(); + let tx_path = "tests/data/annotate/db/grch37/txs.bin.zst"; let tx_db = load_tx_db(tx_path)?; let provider = Arc::new(MehariProvider::new(tx_db, Assembly::Grch37p10)); @@ -725,10 +735,10 @@ mod test { let res = predictor .predict(&VcfVariant { - chromosome: String::from("17"), - position: 41_197_701, - reference: String::from("G"), - alternative: String::from("C"), + chromosome: spdi[0].clone(), + position: spdi[1].parse()?, + reference: spdi[2].clone(), + alternative: spdi[3].clone(), })? .unwrap(); diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant.snap index 8f255518..db216e1b 100644 --- a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant.snap +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant.snap @@ -29,6 +29,6 @@ cds_pos: protein_pos: ord: 1862 total: 1864 -distance: -1390 +distance: ~ messages: ~ From ba2e420bdc449976e9621b30c664ade0f5ec8172 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Fri, 20 Oct 2023 18:27:38 +0200 Subject: [PATCH 2/5] cargo fmt --- src/annotate/seqvars/csq.rs | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/annotate/seqvars/csq.rs b/src/annotate/seqvars/csq.rs index 5627e65a..d95f55af 100644 --- a/src/annotate/seqvars/csq.rs +++ b/src/annotate/seqvars/csq.rs @@ -725,7 +725,11 @@ mod test { fn annotate_snv_brca1_one_variant(#[case] spdi: &str) -> Result<(), anyhow::Error> { crate::common::set_snapshot_suffix!("{}", spdi.replace(":", "-")); - let spdi = spdi.split(":").into_iter().map(|s| s.to_string()).collect::>(); + let spdi = spdi + .split(":") + .into_iter() + .map(|s| s.to_string()) + .collect::>(); let tx_path = "tests/data/annotate/db/grch37/txs.bin.zst"; let tx_db = load_tx_db(tx_path)?; From b6cd35e5ffa361a3033114f3d13a12db8692c3c0 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Fri, 20 Oct 2023 18:40:37 +0200 Subject: [PATCH 3/5] exon works, rest not --- src/annotate/seqvars/csq.rs | 34 +++++++++++++------ ..._test__annotate_snv_brca1_one_variant.snap | 34 ------------------- 2 files changed, 23 insertions(+), 45 deletions(-) delete mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant.snap diff --git a/src/annotate/seqvars/csq.rs b/src/annotate/seqvars/csq.rs index d95f55af..6ebcbd36 100644 --- a/src/annotate/seqvars/csq.rs +++ b/src/annotate/seqvars/csq.rs @@ -165,7 +165,7 @@ impl ConsequencePredictor { let mut rank = Rank::default(); let mut is_exonic = false; let mut is_intronic = false; - let mut distance = None; + let mut distance: Option = None; let mut tx_len = 0; for exon_alignment in &alignment.exons { tx_len += exon_alignment.alt_end_i - exon_alignment.alt_start_i; @@ -185,16 +185,19 @@ impl ConsequencePredictor { }; is_exonic = true; - if var_start <= exon_start || var_end >= exon_end { + if var_start <= exon_end && var_end >= exon_start { // Overlaps with exon/intron boundary. distance = Some(0); } else { let dist_start = -(var_start - exon_start + 1); let dist_end = exon_end - var_end + 1; - if dist_end >= dist_start.abs() { - distance = Some(dist_end); + let dist_start_end = if dist_start.abs() <= dist_end.abs() { + dist_start } else { - distance = Some(dist_start); + dist_end + }; + if distance.is_none() || dist_start_end.abs() <= distance.unwrap().abs() { + distance = Some(dist_start_end); } } } else if let Some(intron_start) = intron_start { @@ -209,10 +212,13 @@ impl ConsequencePredictor { let dist_start = -(var_start - intron_start); let dist_end = intron_end - var_end; - if dist_end <= dist_start.abs() { - distance = Some(dist_end); + let dist_start_end = if dist_start.abs() <= dist_end.abs() { + dist_start } else { - distance = Some(dist_start); + dist_end + }; + if distance.is_none() || dist_start_end.abs() <= distance.unwrap().abs() { + distance = Some(dist_start_end); } } } @@ -339,7 +345,9 @@ impl ConsequencePredictor { Strand::Minus => consequences.push(Consequence::DownstreamGeneVariant), } } - distance = Some(val); + if distance.is_none() { + distance = Some(val); + } } else if is_downstream { let val = var_start - max_end; if val.abs() <= 5_000 { @@ -348,7 +356,9 @@ impl ConsequencePredictor { Strand::Minus => consequences.push(Consequence::UpstreamGeneVariant), } } - distance = Some(val); + if distance.is_none() { + distance = Some(val); + } } let var_g = HgvsVariant::GenomeVariant { @@ -717,11 +727,13 @@ mod test { #[rstest::rstest] #[case("17:41197701:G:C")] + #[case("17:41197697:G:C")] + #[case("17:41197696:G:C")] #[case("17:41197695:G:C")] #[case("17:41197694:G:C")] - #[case("17:41197694:G:C")] #[case("17:41197693:G:C")] #[case("17:41197692:G:C")] + #[case("17:41197691:G:C")] fn annotate_snv_brca1_one_variant(#[case] spdi: &str) -> Result<(), anyhow::Error> { crate::common::set_snapshot_suffix!("{}", spdi.replace(":", "-")); diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant.snap deleted file mode 100644 index db216e1b..00000000 --- a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant.snap +++ /dev/null @@ -1,34 +0,0 @@ ---- -source: src/annotate/seqvars/csq.rs -expression: "res[0]" ---- -allele: - Alt: - alternative: C -consequences: - - missense_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: 23 - total: 23 -hgvs_t: c.5586C>G -hgvs_p: p.H1862Q -tx_pos: - ord: 5699 - total: 7088 -cds_pos: - ord: 5586 - total: 5592 -protein_pos: - ord: 1862 - total: 1864 -distance: ~ -messages: ~ - From c0a26618dd44ffc5365ae59e8e609ecf02dae86b Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Fri, 20 Oct 2023 19:17:40 +0200 Subject: [PATCH 4/5] wip --- src/annotate/seqvars/csq.rs | 51 ++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 29 deletions(-) diff --git a/src/annotate/seqvars/csq.rs b/src/annotate/seqvars/csq.rs index 6ebcbd36..85a5515d 100644 --- a/src/annotate/seqvars/csq.rs +++ b/src/annotate/seqvars/csq.rs @@ -167,7 +167,7 @@ impl ConsequencePredictor { let mut is_intronic = false; let mut distance: Option = None; let mut tx_len = 0; - for exon_alignment in &alignment.exons { + for exon_alignment in &alignment.exons[0..1] { // xxxXXXXxxx tx_len += exon_alignment.alt_end_i - exon_alignment.alt_start_i; let exon_start = exon_alignment.alt_start_i; @@ -184,22 +184,7 @@ impl ConsequencePredictor { total: alignment.exons.len() as i32, }; is_exonic = true; - - if var_start <= exon_end && var_end >= exon_start { - // Overlaps with exon/intron boundary. - distance = Some(0); - } else { - let dist_start = -(var_start - exon_start + 1); - let dist_end = exon_end - var_end + 1; - let dist_start_end = if dist_start.abs() <= dist_end.abs() { - dist_start - } else { - dist_end - }; - if distance.is_none() || dist_start_end.abs() <= distance.unwrap().abs() { - distance = Some(dist_start_end); - } - } + distance = Some(0); } else if let Some(intron_start) = intron_start { if var_start >= intron_start && var_end <= intron_end { // Contained within intron: cannot be in next exon. @@ -210,14 +195,18 @@ impl ConsequencePredictor { }; is_intronic = true; - let dist_start = -(var_start - intron_start); - let dist_end = intron_end - var_end; + // We compute the "distance" with "+1", the first base of the + // intron is "+1", the last one is "-1". + let dist_start = -(var_start + 1 - intron_start); + let dist_end = intron_end + 1 - var_end; let dist_start_end = if dist_start.abs() <= dist_end.abs() { dist_start } else { dist_end }; - if distance.is_none() || dist_start_end.abs() <= distance.unwrap().abs() { + if distance.is_none() + || dist_start_end.abs() <= distance.expect("cannot be None").abs() + { distance = Some(dist_start_end); } } @@ -726,14 +715,18 @@ mod test { } #[rstest::rstest] - #[case("17:41197701:G:C")] - #[case("17:41197697:G:C")] - #[case("17:41197696:G:C")] - #[case("17:41197695:G:C")] - #[case("17:41197694:G:C")] - #[case("17:41197693:G:C")] - #[case("17:41197692:G:C")] - #[case("17:41197691:G:C")] + #[case("17:41197701:G:C")] // exonic + #[case("17:41196309:G:C")] // 3bp 3' upstream + #[case("17:41196310:G:C")] // 2bp 3' upstream + #[case("17:41196311:G:C")] // 1bp 3' upstream + #[case("17:41196312:G:C")] // ex. 3' UTR + #[case("17:41196313:G:C")] // ex. 3' UTR + #[case("17:41197818:G:C")] // exonic + #[case("17:41197819:G:C")] // exonic + #[case("17:41197820:G:C")] // 1bp intronic + #[case("17:41197821:G:C")] // 2bp intronic + #[case("17:41197822:G:C")] // 3bp intronic + #[case("17:41197823:G:C")] // 4bp intronic fn annotate_snv_brca1_one_variant(#[case] spdi: &str) -> Result<(), anyhow::Error> { crate::common::set_snapshot_suffix!("{}", spdi.replace(":", "-")); @@ -759,7 +752,7 @@ mod test { .unwrap(); assert_eq!(res.len(), 4); - insta::assert_yaml_snapshot!(res[0]); + insta::assert_yaml_snapshot!(res); Ok(()) } From 196efc78cfad4f6b05303ad18ce35925d05fc3bb Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Fri, 20 Oct 2023 19:45:41 +0200 Subject: [PATCH 5/5] wip --- src/annotate/seqvars/csq.rs | 53 +++++--- ...snv_brca1_one_variant@17-41196309-G-C.snap | 89 +++++++++++++ ...snv_brca1_one_variant@17-41196310-G-C.snap | 89 +++++++++++++ ...snv_brca1_one_variant@17-41196311-G-C.snap | 89 +++++++++++++ ...snv_brca1_one_variant@17-41196312-G-C.snap | 113 ++++++++++++++++ ...snv_brca1_one_variant@17-41196313-G-C.snap | 113 ++++++++++++++++ ...snv_brca1_one_variant@17-41197701-G-C.snap | 119 +++++++++++++++++ ...snv_brca1_one_variant@17-41197818-G-C.snap | 121 ++++++++++++++++++ ...snv_brca1_one_variant@17-41197819-G-C.snap | 121 ++++++++++++++++++ ...snv_brca1_one_variant@17-41197820-G-C.snap | 117 +++++++++++++++++ ...snv_brca1_one_variant@17-41197821-G-C.snap | 117 +++++++++++++++++ ...snv_brca1_one_variant@17-41197822-G-C.snap | 117 +++++++++++++++++ ...snv_brca1_one_variant@17-41197823-G-C.snap | 117 +++++++++++++++++ ...snv_brca1_one_variant@17-41277379-A-C.snap | 113 ++++++++++++++++ ...snv_brca1_one_variant@17-41277380-G-C.snap | 113 ++++++++++++++++ ...snv_brca1_one_variant@17-41277381-G-T.snap | 113 ++++++++++++++++ ...snv_brca1_one_variant@17-41277382-G-C.snap | 89 +++++++++++++ ...snv_brca1_one_variant@17-41277383-A-C.snap | 89 +++++++++++++ ...snv_brca1_one_variant@17-41277384-G-C.snap | 89 +++++++++++++ 19 files changed, 1963 insertions(+), 18 deletions(-) create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196309-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196310-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196311-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196312-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196313-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197701-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197818-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197819-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197820-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197821-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197822-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197823-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277379-A-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277380-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277381-G-T.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277382-G-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277383-A-C.snap create mode 100644 src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277384-G-C.snap diff --git a/src/annotate/seqvars/csq.rs b/src/annotate/seqvars/csq.rs index 85a5515d..73ffce51 100644 --- a/src/annotate/seqvars/csq.rs +++ b/src/annotate/seqvars/csq.rs @@ -167,7 +167,7 @@ impl ConsequencePredictor { let mut is_intronic = false; let mut distance: Option = None; let mut tx_len = 0; - for exon_alignment in &alignment.exons[0..1] { // xxxXXXXxxx + for exon_alignment in &alignment.exons { tx_len += exon_alignment.alt_end_i - exon_alignment.alt_start_i; let exon_start = exon_alignment.alt_start_i; @@ -186,6 +186,8 @@ impl ConsequencePredictor { is_exonic = true; distance = Some(0); } else if let Some(intron_start) = intron_start { + // We have are in an intron (the first exon does not have an intron left of it + // which is expressed by `intron_start` being an `Option` rather than `i32`. if var_start >= intron_start && var_end <= intron_end { // Contained within intron: cannot be in next exon. if !is_exonic { @@ -197,8 +199,8 @@ impl ConsequencePredictor { // We compute the "distance" with "+1", the first base of the // intron is "+1", the last one is "-1". - let dist_start = -(var_start + 1 - intron_start); - let dist_end = intron_end + 1 - var_end; + let dist_start = var_start + 1 - intron_start; + let dist_end = -(intron_end + 1 - var_end); let dist_start_end = if dist_start.abs() <= dist_end.abs() { dist_start } else { @@ -327,7 +329,7 @@ impl ConsequencePredictor { consequences.push(Consequence::IntronVariant); } } else if is_upstream { - let val = -(min_start - var_end); + let val = -(min_start + 1 - var_end); if val.abs() <= 5_000 { match Strand::try_from(alignment.strand).expect("invalid strand") { Strand::Plus => consequences.push(Consequence::UpstreamGeneVariant), @@ -338,7 +340,7 @@ impl ConsequencePredictor { distance = Some(val); } } else if is_downstream { - let val = var_start - max_end; + let val = var_start + 1 - max_end; if val.abs() <= 5_000 { match Strand::try_from(alignment.strand).expect("invalid strand") { Strand::Plus => consequences.push(Consequence::DownstreamGeneVariant), @@ -715,19 +717,28 @@ mod test { } #[rstest::rstest] - #[case("17:41197701:G:C")] // exonic - #[case("17:41196309:G:C")] // 3bp 3' upstream - #[case("17:41196310:G:C")] // 2bp 3' upstream - #[case("17:41196311:G:C")] // 1bp 3' upstream - #[case("17:41196312:G:C")] // ex. 3' UTR - #[case("17:41196313:G:C")] // ex. 3' UTR - #[case("17:41197818:G:C")] // exonic - #[case("17:41197819:G:C")] // exonic - #[case("17:41197820:G:C")] // 1bp intronic - #[case("17:41197821:G:C")] // 2bp intronic - #[case("17:41197822:G:C")] // 3bp intronic - #[case("17:41197823:G:C")] // 4bp intronic - fn annotate_snv_brca1_one_variant(#[case] spdi: &str) -> Result<(), anyhow::Error> { + #[case("17:41197701:G:C", 0)] // exonic + #[case("17:41196309:G:C", -3)] // 3bp 3' upstream + #[case("17:41196310:G:C", -2)] // 2bp 3' upstream + #[case("17:41196311:G:C", -1)] // 1bp 3' upstream + #[case("17:41196312:G:C", 0)] // ex. 3' UTR + #[case("17:41196313:G:C", 0)] // ex. 3' UTR + #[case("17:41197818:G:C", 0)] // exonic + #[case("17:41197819:G:C", 0)] // exonic + #[case("17:41197820:G:C", 1)] // 1bp intronic + #[case("17:41197821:G:C", 2)] // 2bp intronic + #[case("17:41197822:G:C", 3)] // 3bp intronic + #[case("17:41197823:G:C", 4)] // 4bp intronic + #[case("17:41277379:A:C", 0)] // exonic + #[case("17:41277380:G:C", 0)] // exonic + #[case("17:41277381:G:T", 0)] // exonic + #[case("17:41277382:G:C", 1)] // 1bp upstream + #[case("17:41277383:A:C", 2)] // 2bp upstream + #[case("17:41277384:G:C", 3)] // 3bp upstream + fn annotate_snv_brca1_one_variant( + #[case] spdi: &str, + #[case] expected_dist: i32, + ) -> Result<(), anyhow::Error> { crate::common::set_snapshot_suffix!("{}", spdi.replace(":", "-")); let spdi = spdi @@ -753,6 +764,12 @@ mod test { assert_eq!(res.len(), 4); insta::assert_yaml_snapshot!(res); + assert_eq!( + res[0].distance, + Some(expected_dist), + "spdi = {}", + spdi.join(":") + ); Ok(()) } diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196309-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196309-G-C.snap new file mode 100644 index 00000000..c63b86ba --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196309-G-C.snap @@ -0,0 +1,89 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -3 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -3 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -3 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -3 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196310-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196310-G-C.snap new file mode 100644 index 00000000..fc289eeb --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196310-G-C.snap @@ -0,0 +1,89 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -2 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -2 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -2 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -2 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196311-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196311-G-C.snap new file mode 100644 index 00000000..3dfa1eb2 --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196311-G-C.snap @@ -0,0 +1,89 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -1 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -1 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -1 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - downstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: -1 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196312-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196312-G-C.snap new file mode 100644 index 00000000..d92d49f4 --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196312-G-C.snap @@ -0,0 +1,113 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - 3_prime_UTR_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: 23 + total: 23 + hgvs_t: c.*1383A>G + hgvs_p: p.? + tx_pos: + ord: 7088 + total: 7088 + cds_pos: + ord: 1383 + total: 5592 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 3_prime_UTR_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: 22 + total: 22 + hgvs_t: c.*1383A>G + hgvs_p: p.? + tx_pos: + ord: 7028 + total: 7028 + cds_pos: + ord: 1383 + total: 5451 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 3_prime_UTR_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: 22 + total: 22 + hgvs_t: c.*1489A>G + hgvs_p: p.? + tx_pos: + ord: 3696 + total: 3696 + cds_pos: + ord: 1489 + total: 2100 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 3_prime_UTR_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: 24 + total: 24 + hgvs_t: c.*1383A>G + hgvs_p: p.? + tx_pos: + ord: 7151 + total: 7151 + cds_pos: + ord: 1383 + total: 5655 + protein_pos: ~ + distance: 0 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196313-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196313-G-C.snap new file mode 100644 index 00000000..010a6823 --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41196313-G-C.snap @@ -0,0 +1,113 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - 3_prime_UTR_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: 23 + total: 23 + hgvs_t: c.*1382C>G + hgvs_p: p.? + tx_pos: + ord: 7087 + total: 7088 + cds_pos: + ord: 1382 + total: 5592 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 3_prime_UTR_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: 22 + total: 22 + hgvs_t: c.*1382C>G + hgvs_p: p.? + tx_pos: + ord: 7027 + total: 7028 + cds_pos: + ord: 1382 + total: 5451 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 3_prime_UTR_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: 22 + total: 22 + hgvs_t: c.*1488C>G + hgvs_p: p.? + tx_pos: + ord: 3695 + total: 3696 + cds_pos: + ord: 1488 + total: 2100 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 3_prime_UTR_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: 24 + total: 24 + hgvs_t: c.*1382C>G + hgvs_p: p.? + tx_pos: + ord: 7150 + total: 7151 + cds_pos: + ord: 1382 + total: 5655 + protein_pos: ~ + distance: 0 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197701-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197701-G-C.snap new file mode 100644 index 00000000..6a8f6cdc --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197701-G-C.snap @@ -0,0 +1,119 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - missense_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: 23 + total: 23 + hgvs_t: c.5586C>G + hgvs_p: p.H1862Q + tx_pos: + ord: 5699 + total: 7088 + cds_pos: + ord: 5586 + total: 5592 + protein_pos: + ord: 1862 + total: 1864 + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - missense_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: 22 + total: 22 + hgvs_t: c.5445C>G + hgvs_p: p.H1815Q + tx_pos: + ord: 5639 + total: 7028 + cds_pos: + ord: 5445 + total: 5451 + protein_pos: + ord: 1815 + total: 1817 + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 3_prime_UTR_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: 22 + total: 22 + hgvs_t: c.*100C>G + hgvs_p: p.? + tx_pos: + ord: 2307 + total: 3696 + cds_pos: + ord: 100 + total: 2100 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - missense_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: 24 + total: 24 + hgvs_t: c.5649C>G + hgvs_p: p.H1883Q + tx_pos: + ord: 5762 + total: 7151 + cds_pos: + ord: 5649 + total: 5655 + protein_pos: + ord: 1883 + total: 1885 + distance: 0 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197818-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197818-G-C.snap new file mode 100644 index 00000000..b01a8af0 --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197818-G-C.snap @@ -0,0 +1,121 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - 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 + rank: + ord: 23 + total: 23 + hgvs_t: c.5469A>G + hgvs_p: p.A1823= + tx_pos: + ord: 5582 + total: 7088 + cds_pos: + ord: 5469 + total: 5592 + protein_pos: + ord: 1823 + total: 1864 + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 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: 22 + total: 22 + hgvs_t: c.5328A>G + hgvs_p: p.A1776= + tx_pos: + ord: 5522 + total: 7028 + cds_pos: + ord: 5328 + total: 5451 + protein_pos: + ord: 1776 + total: 1817 + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - missense_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: 22 + total: 22 + hgvs_t: c.2083A>G + hgvs_p: p.N695D + tx_pos: + ord: 2190 + total: 3696 + cds_pos: + ord: 2083 + total: 2100 + protein_pos: + ord: 695 + total: 700 + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 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: 24 + total: 24 + hgvs_t: c.5532A>G + hgvs_p: p.A1844= + tx_pos: + ord: 5645 + total: 7151 + cds_pos: + ord: 5532 + total: 5655 + protein_pos: + ord: 1844 + total: 1885 + distance: 0 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197819-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197819-G-C.snap new file mode 100644 index 00000000..3e39c859 --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197819-G-C.snap @@ -0,0 +1,121 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - missense_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: 23 + total: 23 + hgvs_t: c.5468C>G + hgvs_p: p.A1823G + tx_pos: + ord: 5581 + total: 7088 + cds_pos: + ord: 5468 + total: 5592 + protein_pos: + ord: 1823 + total: 1864 + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - missense_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: 22 + total: 22 + hgvs_t: c.5327C>G + hgvs_p: p.A1776G + tx_pos: + ord: 5521 + total: 7028 + cds_pos: + ord: 5327 + total: 5451 + protein_pos: + ord: 1776 + total: 1817 + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - missense_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: 22 + total: 22 + hgvs_t: c.2082C>G + hgvs_p: p.C694W + tx_pos: + ord: 2189 + total: 3696 + cds_pos: + ord: 2082 + total: 2100 + protein_pos: + ord: 694 + total: 700 + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - missense_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: 24 + total: 24 + hgvs_t: c.5531C>G + hgvs_p: p.A1844G + tx_pos: + ord: 5644 + total: 7151 + cds_pos: + ord: 5531 + total: 5655 + protein_pos: + ord: 1844 + total: 1885 + distance: 0 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197820-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197820-G-C.snap new file mode 100644 index 00000000..642d524a --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197820-G-C.snap @@ -0,0 +1,117 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - splice_acceptor_variant + - intron_variant + putative_impact: HIGH + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 22 + total: 22 + hgvs_t: c.5468-1C>G + hgvs_p: p.? + tx_pos: + ord: 5581 + total: 7088 + cds_pos: + ord: 5468 + total: 5592 + protein_pos: ~ + distance: 1 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_acceptor_variant + - intron_variant + putative_impact: HIGH + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 21 + total: 21 + hgvs_t: c.5327-1C>G + hgvs_p: p.? + tx_pos: + ord: 5521 + total: 7028 + cds_pos: + ord: 5327 + total: 5451 + protein_pos: ~ + distance: 1 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_acceptor_variant + - intron_variant + putative_impact: HIGH + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 21 + total: 21 + hgvs_t: c.2082-1C>G + hgvs_p: p.? + tx_pos: + ord: 2189 + total: 3696 + cds_pos: + ord: 2082 + total: 2100 + protein_pos: ~ + distance: 1 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_acceptor_variant + - intron_variant + putative_impact: HIGH + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 23 + total: 23 + hgvs_t: c.5531-1C>G + hgvs_p: p.? + tx_pos: + ord: 5644 + total: 7151 + cds_pos: + ord: 5531 + total: 5655 + protein_pos: ~ + distance: 1 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197821-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197821-G-C.snap new file mode 100644 index 00000000..8d59d25a --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197821-G-C.snap @@ -0,0 +1,117 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - splice_acceptor_variant + - intron_variant + putative_impact: HIGH + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 22 + total: 22 + hgvs_t: c.5468-2C>G + hgvs_p: p.? + tx_pos: + ord: 5581 + total: 7088 + cds_pos: + ord: 5468 + total: 5592 + protein_pos: ~ + distance: 2 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_acceptor_variant + - intron_variant + putative_impact: HIGH + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 21 + total: 21 + hgvs_t: c.5327-2C>G + hgvs_p: p.? + tx_pos: + ord: 5521 + total: 7028 + cds_pos: + ord: 5327 + total: 5451 + protein_pos: ~ + distance: 2 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_acceptor_variant + - intron_variant + putative_impact: HIGH + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 21 + total: 21 + hgvs_t: c.2082-2C>G + hgvs_p: p.? + tx_pos: + ord: 2189 + total: 3696 + cds_pos: + ord: 2082 + total: 2100 + protein_pos: ~ + distance: 2 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_acceptor_variant + - intron_variant + putative_impact: HIGH + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 23 + total: 23 + hgvs_t: c.5531-2C>G + hgvs_p: p.? + tx_pos: + ord: 5644 + total: 7151 + cds_pos: + ord: 5531 + total: 5655 + protein_pos: ~ + distance: 2 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197822-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197822-G-C.snap new file mode 100644 index 00000000..925ad57b --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197822-G-C.snap @@ -0,0 +1,117 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - splice_region_variant + - intron_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: 22 + total: 22 + hgvs_t: c.5468-3C>G + hgvs_p: p.? + tx_pos: + ord: 5581 + total: 7088 + cds_pos: + ord: 5468 + total: 5592 + protein_pos: ~ + distance: 3 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_region_variant + - intron_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: 21 + total: 21 + hgvs_t: c.5327-3C>G + hgvs_p: p.? + tx_pos: + ord: 5521 + total: 7028 + cds_pos: + ord: 5327 + total: 5451 + protein_pos: ~ + distance: 3 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_region_variant + - intron_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: 21 + total: 21 + hgvs_t: c.2082-3C>G + hgvs_p: p.? + tx_pos: + ord: 2189 + total: 3696 + cds_pos: + ord: 2082 + total: 2100 + protein_pos: ~ + distance: 3 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_region_variant + - intron_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: 23 + total: 23 + hgvs_t: c.5531-3C>G + hgvs_p: p.? + tx_pos: + ord: 5644 + total: 7151 + cds_pos: + ord: 5531 + total: 5655 + protein_pos: ~ + distance: 3 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197823-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197823-G-C.snap new file mode 100644 index 00000000..c1212c6f --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41197823-G-C.snap @@ -0,0 +1,117 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - splice_region_variant + - intron_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: 22 + total: 22 + hgvs_t: c.5468-4C>G + hgvs_p: p.? + tx_pos: + ord: 5581 + total: 7088 + cds_pos: + ord: 5468 + total: 5592 + protein_pos: ~ + distance: 4 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_region_variant + - intron_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: 21 + total: 21 + hgvs_t: c.5327-4C>G + hgvs_p: p.? + tx_pos: + ord: 5521 + total: 7028 + cds_pos: + ord: 5327 + total: 5451 + protein_pos: ~ + distance: 4 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_region_variant + - intron_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: 21 + total: 21 + hgvs_t: c.2082-4C>G + hgvs_p: p.? + tx_pos: + ord: 2189 + total: 3696 + cds_pos: + ord: 2082 + total: 2100 + protein_pos: ~ + distance: 4 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - splice_region_variant + - intron_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: 23 + total: 23 + hgvs_t: c.5531-4C>G + hgvs_p: p.? + tx_pos: + ord: 5644 + total: 7151 + cds_pos: + ord: 5531 + total: 5655 + protein_pos: ~ + distance: 4 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277379-A-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277379-A-C.snap new file mode 100644 index 00000000..0675fc68 --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277379-A-C.snap @@ -0,0 +1,113 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - 5_prime_UTR_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: 1 + total: 23 + hgvs_t: c.-111T>G + hgvs_p: p.? + tx_pos: + ord: 3 + total: 7088 + cds_pos: + ord: -111 + total: 5592 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 5_prime_UTR_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: 1 + total: 22 + hgvs_t: c.-192T>G + hgvs_p: p.? + tx_pos: + ord: 3 + total: 7028 + cds_pos: + ord: -192 + total: 5451 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 5_prime_UTR_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: 1 + total: 22 + hgvs_t: c.-105T>G + hgvs_p: p.? + tx_pos: + ord: 3 + total: 3696 + cds_pos: + ord: -105 + total: 2100 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 5_prime_UTR_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: 1 + total: 24 + hgvs_t: c.-111T>G + hgvs_p: p.? + tx_pos: + ord: 3 + total: 7151 + cds_pos: + ord: -111 + total: 5655 + protein_pos: ~ + distance: 0 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277380-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277380-G-C.snap new file mode 100644 index 00000000..7c7e12d1 --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277380-G-C.snap @@ -0,0 +1,113 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - 5_prime_UTR_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: 1 + total: 23 + hgvs_t: c.-112C>G + hgvs_p: p.? + tx_pos: + ord: 2 + total: 7088 + cds_pos: + ord: -112 + total: 5592 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 5_prime_UTR_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: 1 + total: 22 + hgvs_t: c.-193C>G + hgvs_p: p.? + tx_pos: + ord: 2 + total: 7028 + cds_pos: + ord: -193 + total: 5451 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 5_prime_UTR_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: 1 + total: 22 + hgvs_t: c.-106C>G + hgvs_p: p.? + tx_pos: + ord: 2 + total: 3696 + cds_pos: + ord: -106 + total: 2100 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - 5_prime_UTR_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: 1 + total: 24 + hgvs_t: c.-112C>G + hgvs_p: p.? + tx_pos: + ord: 2 + total: 7151 + cds_pos: + ord: -112 + total: 5655 + protein_pos: ~ + distance: 0 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277381-G-T.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277381-G-T.snap new file mode 100644 index 00000000..d366328b --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277381-G-T.snap @@ -0,0 +1,113 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: T + consequences: + - 5_prime_UTR_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: 1 + total: 23 + hgvs_t: c.-113G>A + hgvs_p: p.? + tx_pos: + ord: 1 + total: 7088 + cds_pos: + ord: -113 + total: 5592 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: T + consequences: + - 5_prime_UTR_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: 1 + total: 22 + hgvs_t: c.-194G>A + hgvs_p: p.? + tx_pos: + ord: 1 + total: 7028 + cds_pos: + ord: -194 + total: 5451 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: T + consequences: + - 5_prime_UTR_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: 1 + total: 22 + hgvs_t: c.-107G>A + hgvs_p: p.? + tx_pos: + ord: 1 + total: 3696 + cds_pos: + ord: -107 + total: 2100 + protein_pos: ~ + distance: 0 + messages: ~ +- allele: + Alt: + alternative: T + consequences: + - 5_prime_UTR_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: 1 + total: 24 + hgvs_t: c.-113G>A + hgvs_p: p.? + tx_pos: + ord: 1 + total: 7151 + cds_pos: + ord: -113 + total: 5655 + protein_pos: ~ + distance: 0 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277382-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277382-G-C.snap new file mode 100644 index 00000000..bbe01b82 --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277382-G-C.snap @@ -0,0 +1,89 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 1 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 1 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 1 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 1 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277383-A-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277383-A-C.snap new file mode 100644 index 00000000..27c0674a --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277383-A-C.snap @@ -0,0 +1,89 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 2 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 2 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 2 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 2 + messages: ~ + diff --git a/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277384-G-C.snap b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277384-G-C.snap new file mode 100644 index 00000000..57627679 --- /dev/null +++ b/src/annotate/seqvars/snapshots/mehari__annotate__seqvars__csq__test__annotate_snv_brca1_one_variant@17-41277384-G-C.snap @@ -0,0 +1,89 @@ +--- +source: src/annotate/seqvars/csq.rs +expression: res +--- +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 3 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 3 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 3 + messages: ~ +- allele: + Alt: + alternative: C + consequences: + - upstream_gene_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: ~ + hgvs_t: ~ + hgvs_p: ~ + tx_pos: ~ + cds_pos: ~ + protein_pos: ~ + distance: 3 + messages: ~ +