diff --git a/protos/annonars/clinvar/minimal.proto b/protos/annonars/clinvar/minimal.proto index f815b750..8fe1fe2b 100644 --- a/protos/annonars/clinvar/minimal.proto +++ b/protos/annonars/clinvar/minimal.proto @@ -4,92 +4,10 @@ syntax = "proto3"; package annonars.clinvar.minimal; -// Enumeration for variant type. -enum VariantType { - // unknown - VARIANT_TYPE_UNKNOWN = 0; - // deletion - VARIANT_TYPE_DELETION = 1; - // duplication - VARIANT_TYPE_DUPLICATION = 2; - // indel - VARIANT_TYPE_INDEL = 3; - // insertion - VARIANT_TYPE_INSERTION = 4; - // inversion - VARIANT_TYPE_INVERSION = 5; - // single nucleotide variant - VARIANT_TYPE_SNV = 6; -} - -// Enumeration for ClinVar pathogenicity. -enum ClinicalSignificance { - // unknown - CLINICAL_SIGNIFICANCE_UNKNOWN = 0; - // Pathogenic. - CLINICAL_SIGNIFICANCE_PATHOGENIC = 1; - // Likely pathogenic. - CLINICAL_SIGNIFICANCE_LIKELY_PATHOGENIC = 2; - // Uncertain significance. - CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE = 3; - // Likely benign. - CLINICAL_SIGNIFICANCE_LIKELY_BENIGN = 4; - // Benign. - CLINICAL_SIGNIFICANCE_BENIGN = 5; -} - -/// Enumeration for ClinVar review status. -enum ReviewStatus { - // unknown - REVIEW_STATUS_PRACTICE_UNKNOWN = 0; - // "practice guideline" - REVIEW_STATUS_PRACTICE_GUIDELINE = 1; - // "reviewed by expert panel" - REVIEW_STATUS_REVIEWED_BY_EXPERT_PANEL = 2; - // "criteria provided, multiple submitters, no conflicts" - REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS = 3; - // "criteria provided, single submitter" - REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER = 4; - // "criteria provided, conflicting interpretations" - REVIEW_STATUS_CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS = 5; - // "no assertion criteria provided" - REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED = 6; - // "no assertion provided" - REVIEW_STATUS_NO_ASSERTION_PROVIDED = 7; - // "flagged submission" - REVIEW_STATUS_FLAGGED_SUBMISSION = 8; - // "no classifications from unflagged records" - REVIEW_STATUS_NO_CLASSIFICATIONS_FROM_UNFLAGGED_RECORDS = 9; -} - -// Record for storing information about a reference clinvar assertion. -message ReferenceAssertion { - // RCV accession identifier. - string rcv = 1; - // Title of the reference assertion, includes phenotype / disease. - string title = 2; - // Clinical significance for variant. - ClinicalSignificance clinical_significance = 3; - // Review status. - ReviewStatus review_status = 4; -} +import "annonars/clinvar_data/extracted_vars.proto"; -// Record for storing minimal information on ClinVar for Mehari. -message Record { - // Genome release. - string release = 1; - // Chromosome name. - string chromosome = 2; - // 1-based start position. - uint32 start = 3; - // 1-based end position. - uint32 stop = 4; - // Reference allele bases in VCF notation. - string reference = 5; - // Alternative allele bases in VCF notation. - string alternative = 6; - // VCV accession identifier. - string vcv = 7; - // The reference assertions, sorted by (ClinicalSignificance, ReviewStatus). - repeated ReferenceAssertion reference_assertions = 8; +// Record with overlap information. +message ExtractedVcvRecordList { + // The list of VCV records that may share a global variant. + repeated clinvar_data.extracted_vars.ExtractedVcvRecord records = 1; } diff --git a/protos/annonars/clinvar/per_gene.proto b/protos/annonars/clinvar/per_gene.proto index 96eae2d3..95090712 100644 --- a/protos/annonars/clinvar/per_gene.proto +++ b/protos/annonars/clinvar/per_gene.proto @@ -4,7 +4,6 @@ syntax = "proto3"; package annonars.clinvar.per_gene; -import "annonars/clinvar/minimal.proto"; import "annonars/clinvar_data/class_by_freq.proto"; import "annonars/clinvar_data/extracted_vars.proto"; import "annonars/clinvar_data/gene_impact.proto"; diff --git a/protos/annonars/clinvar/sv.proto b/protos/annonars/clinvar/sv.proto index 0abfecd0..177f21e6 100644 --- a/protos/annonars/clinvar/sv.proto +++ b/protos/annonars/clinvar/sv.proto @@ -4,46 +4,12 @@ syntax = "proto3"; package annonars.clinvar.sv; -import "annonars/clinvar/minimal.proto"; - -// Record for storing minimal information on ClinVar for Mehari. -message Record { - // Genome release. - string release = 1; - // Chromosome name. - string chromosome = 2; - // 1-based start position. - uint32 start = 3; - // 1-based end position. - uint32 stop = 4; - - // Reference allele bases in VCF notation; optional. - optional string reference = 5; - // Alternative allele bases in VCF notation; optional. - optional string alternative = 6; - - // 1-based inner start position. - optional uint32 inner_start = 7; - // 1-based inner stop position. - optional uint32 inner_stop = 8; - // 1-based outer start position. - optional uint32 outer_start = 9; - // 1-based outer stop position. - optional uint32 outer_stop = 10; - - // The variant type. - annonars.clinvar.minimal.VariantType variant_type = 11; - - // VCV accession identifier. - string vcv = 12; - // The reference assertions, sorted by (ClinicalSignificance, ReviewStatus). - repeated annonars.clinvar.minimal.ReferenceAssertion reference_assertions = 13; -} +import "annonars/clinvar_data/extracted_vars.proto"; // Record with overlap information. message ResponseRecord { // The record. - Record record = 1; + clinvar_data.extracted_vars.ExtractedVcvRecord record = 1; // The reciprocal overlap with the query. double overlap = 2; } diff --git a/src/clinvar_minimal/cli/import.rs b/src/clinvar_minimal/cli/import.rs index fa54de18..e9706e1c 100644 --- a/src/clinvar_minimal/cli/import.rs +++ b/src/clinvar_minimal/cli/import.rs @@ -5,15 +5,11 @@ use std::{io::BufRead, sync::Arc}; use clap::Parser; use prost::Message; -use crate::{ - clinvar_minimal, - common::{self, keys}, - pbs::clinvar::minimal::ReferenceAssertion, -}; +use crate::common::{self, keys}; /// Command line arguments for `clinvar-minimal import` sub command. #[derive(Parser, Debug, Clone)] -#[command(about = "import minimal ClinVar data into RocksDB", long_about = None)] +#[command(about = "import extracted seqvars ClinVar data into RocksDB", long_about = None)] pub struct Args { /// Genome build to use in the build. #[arg(long, value_enum)] @@ -57,7 +53,10 @@ fn jsonl_import( for line in reader.lines() { let line = line?; - let record = match serde_json::from_str::(&line) { + let vcv_record = match serde_json::from_str::< + crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord, + >(&line) + { Ok(record) => record, Err(e) => { tracing::warn!("skipping line because of error: {}", e); @@ -65,32 +64,31 @@ fn jsonl_import( } }; - let clinvar_minimal::cli::reading::Record { - rcv, - vcv, - title, - clinical_significance, - review_status, + let crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord { + accession, + rcvs: rcv_records, sequence_location, .. - } = record; - let clinical_significance: crate::pbs::clinvar::minimal::ClinicalSignificance = - clinical_significance.into(); - let review_status: crate::pbs::clinvar::minimal::ReviewStatus = review_status.into(); - let clinvar_minimal::cli::reading::SequenceLocation { - assembly, + } = vcv_record.clone(); + let accession = accession.expect("accession is required"); + let vcv = format!("{}.{}", accession.accession, accession.version); + let sequence_location = sequence_location.expect("sequence_location is required"); + let crate::pbs::clinvar_data::clinvar_public::location::SequenceLocation { chr, start, - stop, reference_allele_vcf, alternate_allele_vcf, .. } = sequence_location; - if let (Some(start), Some(stop), Some(reference_allele_vcf), Some(alternate_allele_vcf)) = - (start, stop, reference_allele_vcf, alternate_allele_vcf) + let chr_pb = + crate::pbs::clinvar_data::clinvar_public::Chromosome::try_from(chr).map_err(|e| { + anyhow::anyhow!("problem converting chromosome {} to Chromosome: {}", chr, e) + })?; + if let (Some(start), Some(reference_allele_vcf), Some(alternate_allele_vcf)) = + (start, reference_allele_vcf, alternate_allele_vcf) { let var = keys::Var::from( - &chr, + &chr_pb.as_chr_name(), start as i32, &reference_allele_vcf, &alternate_allele_vcf, @@ -106,41 +104,36 @@ fn jsonl_import( continue; } Ok(data) => { - db.put_cf(&cf_by_accession, rcv.as_bytes(), &key)?; db.put_cf(&cf_by_accession, vcv.as_bytes(), &key)?; - - let record = if let Some(data) = data { - let mut record = crate::pbs::clinvar::minimal::Record::decode(&data[..])?; - record.reference_assertions.push( - crate::pbs::clinvar::minimal::ReferenceAssertion { - rcv, - title, - clinical_significance: clinical_significance.into(), - review_status: review_status.into(), - }, - ); - record - .reference_assertions - .sort_by_key(|a| (a.clinical_significance, a.review_status)); + for rcv_record in &rcv_records { + let accession = rcv_record + .accession + .as_ref() + .expect("rcv.accession is required"); + let rcv = format!("{}.{}", accession.accession, accession.version); + db.put_cf(&cf_by_accession, rcv.as_bytes(), &key)?; + } + + let new_record = if let Some(data) = data { + let mut record = + crate::pbs::clinvar::minimal::ExtractedVcvRecordList::decode( + &data[..], + )?; + record.records.push(vcv_record); + record.records.sort_by_key(|a| { + a.accession + .as_ref() + .expect("accession is required") + .accession + .clone() + }); record } else { - crate::pbs::clinvar::minimal::Record { - release: assembly, - chromosome: chr, - start, - stop, - reference: reference_allele_vcf, - alternative: alternate_allele_vcf, - vcv, - reference_assertions: vec![ReferenceAssertion { - rcv, - title, - clinical_significance: clinical_significance.into(), - review_status: review_status.into(), - }], + crate::pbs::clinvar::minimal::ExtractedVcvRecordList { + records: vec![vcv_record], } }; - let buf = record.encode_to_vec(); + let buf = new_record.encode_to_vec(); db.put_cf(&cf_data, &key, &buf)?; } } diff --git a/src/clinvar_minimal/cli/mod.rs b/src/clinvar_minimal/cli/mod.rs index b4b20cc5..e4aad4cc 100644 --- a/src/clinvar_minimal/cli/mod.rs +++ b/src/clinvar_minimal/cli/mod.rs @@ -2,4 +2,3 @@ pub mod import; pub mod query; -pub mod reading; diff --git a/src/clinvar_minimal/cli/query.rs b/src/clinvar_minimal/cli/query.rs index 4039f8ac..cf58dc27 100644 --- a/src/clinvar_minimal/cli/query.rs +++ b/src/clinvar_minimal/cli/query.rs @@ -93,11 +93,13 @@ pub fn open_rocksdb_from_args( fn print_record( out_writer: &mut Box, output_format: common::cli::OutputFormat, - value: &crate::pbs::clinvar::minimal::Record, + value: &crate::pbs::clinvar::minimal::ExtractedVcvRecordList, ) -> Result<(), anyhow::Error> { - match output_format { - common::cli::OutputFormat::Jsonl => { - writeln!(out_writer, "{}", serde_json::to_string(value)?)?; + for record in &value.records { + match output_format { + common::cli::OutputFormat::Jsonl => { + writeln!(out_writer, "{}", serde_json::to_string(record)?)?; + } } } @@ -110,7 +112,7 @@ pub fn query_for_variant( meta: &Meta, db: &rocksdb::DBWithThreadMode, cf_data: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { // Split off the genome release (checked) and convert to key as used in database. let query = spdi::Var { sequence: extract_chrom::from_var(variant, Some(&meta.genome_release))?, @@ -126,8 +128,10 @@ pub fn query_for_variant( raw_value .map(|raw_value| { // Decode via prost. - crate::pbs::clinvar::minimal::Record::decode(&mut std::io::Cursor::new(&raw_value)) - .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) + crate::pbs::clinvar::minimal::ExtractedVcvRecordList::decode(&mut std::io::Cursor::new( + &raw_value, + )) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) }) .transpose() } @@ -138,7 +142,7 @@ pub fn query_for_accession( db: &rocksdb::DBWithThreadMode, cf_data: &Arc, cf_data_by_rsid: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { let accession = accession.to_uppercase(); // VCV*, RCV* // First, lookup accession. @@ -154,8 +158,10 @@ pub fn query_for_accession( raw_value .map(|raw_value| { // Decode via prost. - crate::pbs::clinvar::minimal::Record::decode(&mut std::io::Cursor::new(&raw_value)) - .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) + crate::pbs::clinvar::minimal::ExtractedVcvRecordList::decode(&mut std::io::Cursor::new( + &raw_value, + )) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) }) .transpose() } @@ -246,7 +252,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> } } - let record = crate::pbs::clinvar::minimal::Record::decode( + let record = crate::pbs::clinvar::minimal::ExtractedVcvRecordList::decode( &mut std::io::Cursor::new(&raw_value), ) .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; @@ -277,7 +283,7 @@ mod test { verbose: clap_verbosity_flag::Verbosity::new(1, 0), }; let args = Args { - path_rocksdb: String::from("tests/clinvar-minimal/clinvar-seqvars-grch37-tgds.tsv.db"), + path_rocksdb: String::from("tests/clinvar-minimal/clinvar-seqvars-grch37-tgds.db"), cf_name: String::from("clinvar"), cf_name_by_accession: String::from("clinvar_by_accession"), out_file: temp.join("out").to_string_lossy().to_string(), @@ -369,7 +375,7 @@ mod test { #[test] fn smoke_query_range_find_none_smaller() -> Result<(), anyhow::Error> { let (common, args, _temp) = args(ArgsQuery { - range: Some(spdi::Range::from_str("GRCh37:13:1:95227054")?), + range: Some(spdi::Range::from_str("GRCh37:13:1:95227038")?), ..Default::default() }); run(&common, &args)?; @@ -394,8 +400,8 @@ mod test { #[rstest::rstest] #[test] - #[case("RCV001679107")] - #[case("VCV001307216")] + #[case("RCV001679107.1")] + #[case("VCV001307216.2")] fn smoke_query_by_accession(#[case] accession: &str) -> Result<(), anyhow::Error> { crate::common::set_snapshot_suffix!("{}", &accession); diff --git a/src/clinvar_minimal/cli/reading.rs b/src/clinvar_minimal/cli/reading.rs deleted file mode 100644 index 0d92700e..00000000 --- a/src/clinvar_minimal/cli/reading.rs +++ /dev/null @@ -1,378 +0,0 @@ -//! Reading `clinvar-data-jsonl` variant files. -//! -//! This code is shared for all reading of ClinVar JSONL data. - -use std::{fmt::Display, str::FromStr}; - -use serde::{Deserialize, Serialize}; - -/// Enumeration for ClinVar variant types. -#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)] -pub enum VariantType { - /// Deletion - Deletion, - /// Duplication - Duplication, - /// Indel - Indel, - /// Insertion - Insertion, - /// Inversion - Inversion, - /// Snv - Snv, -} - -impl Display for VariantType { - fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { - match self { - VariantType::Deletion => write!(f, "deletion"), - VariantType::Duplication => write!(f, "duplication"), - VariantType::Indel => write!(f, "indel"), - VariantType::Insertion => write!(f, "insertion"), - VariantType::Inversion => write!(f, "inversion"), - VariantType::Snv => write!(f, "single nucleotide variant"), - } - } -} - -impl FromStr for VariantType { - type Err = anyhow::Error; - - fn from_str(s: &str) -> Result { - Ok(match s { - "copy number loss" | "deletion" => VariantType::Deletion, - "copy number gain" | "duplication" | "tandem duplication" => VariantType::Duplication, - "indel" => VariantType::Indel, - "insertion" => VariantType::Insertion, - "inversion" => VariantType::Inversion, - "single nucleotide variant" => VariantType::Snv, - _ => anyhow::bail!("Unknown variant type: {}", s), - }) - } -} - -impl Serialize for VariantType { - fn serialize(&self, serializer: S) -> Result - where - S: serde::Serializer, - { - serializer.serialize_str(&self.to_string()) - } -} - -impl<'de> Deserialize<'de> for VariantType { - fn deserialize(d: D) -> Result - where - D: serde::Deserializer<'de>, - { - let s = String::deserialize(d)?; - Self::from_str(&s).map_err(serde::de::Error::custom) - } -} - -impl From for crate::pbs::clinvar::minimal::VariantType { - fn from(value: VariantType) -> Self { - match value { - VariantType::Deletion => crate::pbs::clinvar::minimal::VariantType::Deletion, - VariantType::Duplication => crate::pbs::clinvar::minimal::VariantType::Duplication, - VariantType::Indel => crate::pbs::clinvar::minimal::VariantType::Indel, - VariantType::Insertion => crate::pbs::clinvar::minimal::VariantType::Insertion, - VariantType::Inversion => crate::pbs::clinvar::minimal::VariantType::Inversion, - VariantType::Snv => crate::pbs::clinvar::minimal::VariantType::Snv, - } - } -} - -impl From for VariantType { - fn from(value: i32) -> Self { - match value { - 1 => VariantType::Deletion, - 2 => VariantType::Duplication, - 3 => VariantType::Indel, - 4 => VariantType::Insertion, - 5 => VariantType::Inversion, - 6 => VariantType::Snv, - _ => unreachable!(), - } - } -} - -/// Enumeration for ClinVar clinical significance for (de)serialization. -#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)] -pub enum ClinicalSignificance { - /// Pathogenic. - Pathogenic, - /// Likely pathogenic. - LikelyPathogenic, - /// Uncertain significance. - UncertainSignificance, - /// Likely benign. - LikelyBenign, - /// Benign. - Benign, -} - -impl Display for ClinicalSignificance { - fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { - match self { - ClinicalSignificance::Pathogenic => write!(f, "pathogenic"), - ClinicalSignificance::LikelyPathogenic => write!(f, "likely pathogenic"), - ClinicalSignificance::UncertainSignificance => write!(f, "uncertain significance"), - ClinicalSignificance::LikelyBenign => write!(f, "likely benign"), - ClinicalSignificance::Benign => write!(f, "benign"), - } - } -} - -impl FromStr for ClinicalSignificance { - type Err = anyhow::Error; - - fn from_str(s: &str) -> Result { - Ok(match s { - "pathogenic" => ClinicalSignificance::Pathogenic, - "likely pathogenic" => ClinicalSignificance::LikelyPathogenic, - "uncertain significance" => ClinicalSignificance::UncertainSignificance, - "likely benign" => ClinicalSignificance::LikelyBenign, - "benign" => ClinicalSignificance::Benign, - _ => anyhow::bail!("Unknown pathogenicity: {}", s), - }) - } -} - -impl Serialize for ClinicalSignificance { - fn serialize(&self, serializer: S) -> Result - where - S: serde::Serializer, - { - serializer.serialize_str(&self.to_string()) - } -} - -impl<'de> Deserialize<'de> for ClinicalSignificance { - fn deserialize(d: D) -> Result - where - D: serde::Deserializer<'de>, - { - let s = String::deserialize(d)?; - Self::from_str(&s).map_err(serde::de::Error::custom) - } -} - -impl From for crate::pbs::clinvar::minimal::ClinicalSignificance { - fn from(value: ClinicalSignificance) -> Self { - match value { - ClinicalSignificance::Pathogenic => { - crate::pbs::clinvar::minimal::ClinicalSignificance::Pathogenic - } - ClinicalSignificance::LikelyPathogenic => { - crate::pbs::clinvar::minimal::ClinicalSignificance::LikelyPathogenic - } - ClinicalSignificance::UncertainSignificance => { - crate::pbs::clinvar::minimal::ClinicalSignificance::UncertainSignificance - } - ClinicalSignificance::LikelyBenign => { - crate::pbs::clinvar::minimal::ClinicalSignificance::LikelyBenign - } - ClinicalSignificance::Benign => { - crate::pbs::clinvar::minimal::ClinicalSignificance::Benign - } - } - } -} - -impl From for ClinicalSignificance { - fn from(value: i32) -> Self { - match value { - 1 => ClinicalSignificance::Pathogenic, - 2 => ClinicalSignificance::LikelyPathogenic, - 3 => ClinicalSignificance::UncertainSignificance, - 4 => ClinicalSignificance::LikelyBenign, - 5 => ClinicalSignificance::Benign, - _ => unreachable!(), - } - } -} - -/// Enumeration for ClinVar review status for (de)serialization. -#[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord)] -pub enum ReviewStatus { - /// "practice guideline" - PracticeGuideline, - /// "reviewed by expert panel" - ReviewedByExpertPanel, - /// "criteria provided, multiple submitters, no conflicts" - CriteriaProvidedMultipleSubmittersNoConflicts, - /// "criteria provided, single submitter" - CriteriaProvidedSingleSubmitter, - /// "criteria provided, conflicting interpretations" - CriteriaProvidedConflictingInterpretations, - /// "no assertion criteria provided" - NoAssertionCriteriaProvided, - /// "no assertion provided" - NoAssertionProvided, - /// "flagged submission", - FlaggedSubmission, - /// "no classifications from unflagged records", - NoClassificationsFromUnflaggedRecords, -} - -impl Display for ReviewStatus { - fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { - match self { - ReviewStatus::CriteriaProvidedConflictingInterpretations => { - write!(f, "criteria provided, conflicting interpretations") - } - ReviewStatus::CriteriaProvidedMultipleSubmittersNoConflicts => { - write!(f, "criteria provided, multiple submitters, no conflicts") - } - ReviewStatus::CriteriaProvidedSingleSubmitter => { - write!(f, "criteria provided, single submitter") - } - ReviewStatus::NoAssertionCriteriaProvided => { - write!(f, "no assertion criteria provided") - } - ReviewStatus::NoAssertionProvided => write!(f, "no assertion provided"), - ReviewStatus::PracticeGuideline => write!(f, "practice guideline"), - ReviewStatus::ReviewedByExpertPanel => write!(f, "reviewed by expert panel"), - ReviewStatus::FlaggedSubmission => write!(f, "flagged submission"), - ReviewStatus::NoClassificationsFromUnflaggedRecords => { - write!(f, "no classifications from unflagged records") - } - } - } -} - -impl FromStr for ReviewStatus { - type Err = anyhow::Error; - - fn from_str(s: &str) -> Result { - match s { - "criteria provided, conflicting interpretations" => { - Ok(ReviewStatus::CriteriaProvidedConflictingInterpretations) - } - "criteria provided, multiple submitters, no conflicts" => { - Ok(ReviewStatus::CriteriaProvidedMultipleSubmittersNoConflicts) - } - "criteria provided, single submitter" => { - Ok(ReviewStatus::CriteriaProvidedSingleSubmitter) - } - "no assertion criteria provided" => Ok(ReviewStatus::NoAssertionCriteriaProvided), - "no assertion provided" => Ok(ReviewStatus::NoAssertionProvided), - "practice guideline" => Ok(ReviewStatus::PracticeGuideline), - "reviewed by expert panel" => Ok(ReviewStatus::ReviewedByExpertPanel), - "flagged submission" => Ok(ReviewStatus::FlaggedSubmission), - "no classifications from unflagged records" => { - Ok(ReviewStatus::NoClassificationsFromUnflaggedRecords) - } - _ => anyhow::bail!("Unknown review status: {}", s), - } - } -} - -impl Serialize for ReviewStatus { - fn serialize(&self, serializer: S) -> Result - where - S: serde::Serializer, - { - serializer.serialize_str(&self.to_string()) - } -} - -impl<'de> Deserialize<'de> for ReviewStatus { - fn deserialize(d: D) -> Result - where - D: serde::Deserializer<'de>, - { - let s = String::deserialize(d)?; - Self::from_str(&s).map_err(serde::de::Error::custom) - } -} - -impl From for crate::pbs::clinvar::minimal::ReviewStatus { - fn from(value: ReviewStatus) -> Self { - match value { - ReviewStatus::NoAssertionProvided => crate::pbs::clinvar::minimal::ReviewStatus::NoAssertionProvided, - ReviewStatus::NoAssertionCriteriaProvided => { - crate::pbs::clinvar::minimal::ReviewStatus::NoAssertionCriteriaProvided - } - ReviewStatus::CriteriaProvidedConflictingInterpretations => { - crate::pbs::clinvar::minimal::ReviewStatus::CriteriaProvidedConflictingInterpretations - } - ReviewStatus::CriteriaProvidedSingleSubmitter => { - crate::pbs::clinvar::minimal::ReviewStatus::CriteriaProvidedSingleSubmitter - } - ReviewStatus::CriteriaProvidedMultipleSubmittersNoConflicts => { - crate::pbs::clinvar::minimal::ReviewStatus::CriteriaProvidedMultipleSubmittersNoConflicts - } - ReviewStatus::ReviewedByExpertPanel => crate::pbs::clinvar::minimal::ReviewStatus::ReviewedByExpertPanel, - ReviewStatus::PracticeGuideline => crate::pbs::clinvar::minimal::ReviewStatus::PracticeGuideline, - ReviewStatus::FlaggedSubmission => crate::pbs::clinvar::minimal::ReviewStatus::FlaggedSubmission, - ReviewStatus::NoClassificationsFromUnflaggedRecords => crate::pbs::clinvar::minimal::ReviewStatus::NoClassificationsFromUnflaggedRecords, - } - } -} - -impl From for ReviewStatus { - fn from(value: i32) -> Self { - match value { - 1 => ReviewStatus::PracticeGuideline, - 2 => ReviewStatus::ReviewedByExpertPanel, - 3 => ReviewStatus::CriteriaProvidedMultipleSubmittersNoConflicts, - 4 => ReviewStatus::CriteriaProvidedSingleSubmitter, - 5 => ReviewStatus::CriteriaProvidedConflictingInterpretations, - 6 => ReviewStatus::NoAssertionCriteriaProvided, - 7 => ReviewStatus::NoAssertionProvided, - 8 => ReviewStatus::FlaggedSubmission, - 9 => ReviewStatus::NoClassificationsFromUnflaggedRecords, - _ => unreachable!(), - } - } -} - -/// Representation of a record from the `clinvar-data-jsonl` output. -#[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq)] -pub struct Record { - /// RCV accession identifier. - pub rcv: String, - /// VCV accession identifier. - pub vcv: String, - /// RCV title. - pub title: String, - /// HGNC ids - pub hgnc_ids: Vec, - /// The variant type. - pub variant_type: VariantType, - /// ClinVar clinical significance - pub clinical_significance: ClinicalSignificance, - /// ClinVar review status - pub review_status: ReviewStatus, - /// Sequence location - pub sequence_location: SequenceLocation, -} - -/// Representation of a sequence location record. -#[derive(Serialize, Deserialize, Debug, Clone, PartialEq, Eq)] -pub struct SequenceLocation { - /// Genome release. - pub assembly: String, - /// Chromosome name. - pub chr: String, - /// 1-based start position. - pub start: Option, - /// 1-based stop position. - pub stop: Option, - /// Reference allele bases in VCF notation. - pub reference_allele_vcf: Option, - /// Alternative allele bases in VCF notation. - pub alternate_allele_vcf: Option, - - /// 1-based inner start position. - pub inner_start: Option, - /// 1-based inner stop position. - pub inner_stop: Option, - /// 1-based outer start position. - pub outer_start: Option, - /// 1-based outer stop position. - pub outer_stop: Option, -} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_all.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_all.snap index c12c2ba0..61c4bb3c 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_all.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_all.snap @@ -2,73 +2,93 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95227055,"stop":95227055,"reference":"A","alternative":"G","vcv":"VCV001309690","referenceAssertions":[{"rcv":"RCV001756758","title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227093,"stop":95227093,"reference":"T","alternative":"C","vcv":"VCV000792370","referenceAssertions":[{"rcv":"RCV000975465","title":"NM_014305.4(TGDS):c.996A>G (p.Arg332=) AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227114,"stop":95227114,"reference":"G","alternative":"A","vcv":"VCV000720702","referenceAssertions":[{"rcv":"RCV000894054","title":"NM_014305.4(TGDS):c.983-8C>T AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227128,"stop":95227129,"reference":"C","alternative":"CA","vcv":"VCV001261515","referenceAssertions":[{"rcv":"RCV001674093","title":"NM_014305.4(TGDS):c.983-34dup AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227129,"stop":95227129,"reference":"CA","alternative":"C","vcv":"VCV001244089","referenceAssertions":[{"rcv":"RCV001648355","title":"NM_014305.4(TGDS):c.983-23del AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227139,"stop":95227141,"reference":"AAAG","alternative":"A","vcv":"VCV001282312","referenceAssertions":[{"rcv":"RCV001695704","title":"NM_014305.4(TGDS):c.983-35_983-33del AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227140,"stop":95227141,"reference":"AAG","alternative":"A","vcv":"VCV001228958","referenceAssertions":[{"rcv":"RCV001616589","title":"NM_014305.4(TGDS):c.983-35_983-34del AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227340,"stop":95227340,"reference":"C","alternative":"T","vcv":"VCV001288190","referenceAssertions":[{"rcv":"RCV001707165","title":"NM_014305.4(TGDS):c.983-234G>A AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95228593,"stop":95228593,"reference":"A","alternative":"G","vcv":"VCV001575281","referenceAssertions":[{"rcv":"RCV002083442","title":"NM_014305.4(TGDS):c.957T>C (p.Pro319=) AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95228658,"stop":95228658,"reference":"T","alternative":"C","vcv":"VCV000162460","referenceAssertions":[{"rcv":"RCV000149822","title":"NM_014305.4(TGDS):c.892A>G (p.Asn298Asp) AND Catel-Manzke syndrome","clinicalSignificance":"CLINICAL_SIGNIFICANCE_PATHOGENIC","reviewStatus":"REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED"}]} -{"release":"GRCh37","chromosome":"13","start":95228667,"stop":95228667,"reference":"T","alternative":"G","vcv":"VCV002437068","referenceAssertions":[{"rcv":"RCV003140988","title":"NM_014305.4(TGDS):c.885-2A>C AND Catel-Manzke syndrome","clinicalSignificance":"CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95229675,"stop":95229675,"reference":"C","alternative":"G","vcv":"VCV002278206","referenceAssertions":[{"rcv":"RCV002822699","title":"NM_014305.4(TGDS):c.834G>C (p.Glu278Asp) AND Inborn genetic diseases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95229697,"stop":95229697,"reference":"A","alternative":"G","vcv":"VCV001617317","referenceAssertions":[{"rcv":"RCV002076513","title":"NM_014305.4(TGDS):c.826-14T>C AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95229735,"stop":95229735,"reference":"A","alternative":"G","vcv":"VCV001260430","referenceAssertions":[{"rcv":"RCV001669248","title":"NM_014305.4(TGDS):c.826-52T>C AND not 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-{"release":"GRCh37","chromosome":"13","start":95230291,"stop":95230291,"reference":"C","alternative":"T","vcv":"VCV002246034","referenceAssertions":[{"rcv":"RCV002738091","title":"NM_014305.4(TGDS):c.793G>A (p.Val265Ile) AND Inborn genetic diseases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95230343,"stop":95230343,"reference":"T","alternative":"C","vcv":"VCV001932516","referenceAssertions":[{"rcv":"RCV002605801","title":"NM_014305.4(TGDS):c.741A>G (p.Lys247=) AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95230370,"stop":95230370,"reference":"A","alternative":"C","vcv":"VCV000741988","referenceAssertions":[{"rcv":"RCV000918201","title":"NM_014305.4(TGDS):c.714T>G (p.Val238=) AND not 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-{"release":"GRCh37","chromosome":"13","start":95230624,"stop":95230625,"reference":"A","alternative":"AAGTGGCAAACATATT","vcv":"VCV001241711","referenceAssertions":[{"rcv":"RCV001645456","title":"NM_014305.4(TGDS):c.660-201_660-200insCACTAATATGTTTGC AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95230877,"stop":95230877,"reference":"G","alternative":"A","vcv":"VCV001244948","referenceAssertions":[{"rcv":"RCV001649156","title":"NM_014305.4(TGDS):c.659+107C>T AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95230976,"stop":95230976,"reference":"T","alternative":"C","vcv":"VCV000738027","referenceAssertions":[{"rcv":"RCV000913870","title":"NM_014305.4(TGDS):c.659+8A>G AND not 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-{"release":"GRCh37","chromosome":"13","start":95235329,"stop":95235329,"reference":"A","alternative":"G","vcv":"VCV001926065","referenceAssertions":[{"rcv":"RCV002605013","title":"NM_014305.4(TGDS):c.456+19T>C AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95235339,"stop":95235339,"reference":"T","alternative":"G","vcv":"VCV000792360","referenceAssertions":[{"rcv":"RCV000975453","title":"NM_014305.4(TGDS):c.456+9A>C AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95235365,"stop":95235365,"reference":"C","alternative":"A","vcv":"VCV001962614","referenceAssertions":[{"rcv":"RCV002726264","title":"NM_014305.4(TGDS):c.439G>T (p.Gly147Cys) AND not 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-{"release":"GRCh37","chromosome":"13","start":95235557,"stop":95235557,"reference":"A","alternative":"G","vcv":"VCV001273284","referenceAssertions":[{"rcv":"RCV001679107","title":"NM_014305.4(TGDS):c.314-67T>C AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95235626,"stop":95235626,"reference":"A","alternative":"T","vcv":"VCV001294950","referenceAssertions":[{"rcv":"RCV001721615","title":"NM_014305.4(TGDS):c.314-136T>A AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95243106,"stop":95243106,"reference":"C","alternative":"T","vcv":"VCV001878395","referenceAssertions":[{"rcv":"RCV002510448","title":"NM_014305.4(TGDS):c.313+1G>A AND Catel-Manzke 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'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."},"type":"public definition"}}],"xrefs":[{"db":"MedGen","id":"C3661900"}]}],"type":"TYPE_DISEASE","id":"9460","contributesToAggregateClassification":true}],"dateLastEvaluated":"2021-05-22T00:00:00+00:00","dateCreated":"2021-09-24T00:00:00+00:00","mostRecentSubmission":"2023-10-07T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95248751,"stop":95248751,"displayStart":95248751,"displayStop":95248751,"variantLength":1,"positionVcf":95248751,"referenceAlleleVcf":"C","alternateAlleleVcf":"T"},"hgncIds":["HGNC:20324"]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@RCV001679107.1.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@RCV001679107.1.snap new file mode 100644 index 00000000..157aacdb --- /dev/null +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@RCV001679107.1.snap @@ -0,0 +1,5 @@ +--- +source: src/clinvar_minimal/cli/query.rs +expression: "&out_data" +--- +{"accession":{"accession":"VCV001273284","version":1},"rcvs":[{"accession":{"accession":"RCV001679107","version":1},"title":"NM_014305.4(TGDS):c.314-67T>C AND not provided"}],"name":"NM_014305.4(TGDS):c.314-67T>C","variationType":"VARIATION_TYPE_SNV","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Benign","conditions":[{"traits":[{"names":[{"value":"not provided","type":"Preferred","xrefs":[{"db":"Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre","id":"13DG0619"}]},{"value":"none provided","type":"Alternate"}],"attributes":[{"attribute":{"base":{"value":"The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."},"type":"public definition"}}],"xrefs":[{"db":"MedGen","id":"C3661900"}]}],"type":"TYPE_DISEASE","id":"9460","contributesToAggregateClassification":true}],"dateLastEvaluated":"2021-05-15T00:00:00+00:00","dateCreated":"2021-09-24T00:00:00+00:00","mostRecentSubmission":"2021-09-24T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95235557,"stop":95235557,"displayStart":95235557,"displayStop":95235557,"variantLength":1,"positionVcf":95235557,"referenceAlleleVcf":"A","alternateAlleleVcf":"G"},"hgncIds":["HGNC:20324"]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@VCV001307216.2.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@VCV001307216.2.snap new file mode 100644 index 00000000..b0d633a3 --- /dev/null +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_by_accession@VCV001307216.2.snap @@ -0,0 +1,5 @@ +--- +source: src/clinvar_minimal/cli/query.rs +expression: "&out_data" +--- +{"accession":{"accession":"VCV001307216","version":2},"rcvs":[{"accession":{"accession":"RCV001760634","version":2},"title":"NM_014305.4(TGDS):c.582T>G (p.Ser194Arg) AND not provided"}],"name":"NM_014305.4(TGDS):c.582T>G (p.Ser194Arg)","variationType":"VARIATION_TYPE_SNV","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Uncertain significance","conditions":[{"traits":[{"names":[{"value":"not provided","type":"Preferred","xrefs":[{"db":"Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre","id":"13DG0619"}]},{"value":"none provided","type":"Alternate"}],"attributes":[{"attribute":{"base":{"value":"The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."},"type":"public definition"}}],"xrefs":[{"db":"MedGen","id":"C3661900"}]}],"type":"TYPE_DISEASE","id":"9460","contributesToAggregateClassification":true}],"dateLastEvaluated":"2020-12-22T00:00:00+00:00","dateCreated":"2021-11-06T00:00:00+00:00","mostRecentSubmission":"2023-03-04T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95232181,"stop":95232181,"displayStart":95232181,"displayStop":95232181,"variantLength":1,"positionVcf":95232181,"referenceAlleleVcf":"A","alternateAlleleVcf":"C"},"hgncIds":["HGNC:20324"]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_all.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_all.snap index c12c2ba0..e4f99df3 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_all.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_all.snap @@ -2,73 +2,90 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95227055,"stop":95227055,"reference":"A","alternative":"G","vcv":"VCV001309690","referenceAssertions":[{"rcv":"RCV001756758","title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227093,"stop":95227093,"reference":"T","alternative":"C","vcv":"VCV000792370","referenceAssertions":[{"rcv":"RCV000975465","title":"NM_014305.4(TGDS):c.996A>G (p.Arg332=) AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227114,"stop":95227114,"reference":"G","alternative":"A","vcv":"VCV000720702","referenceAssertions":[{"rcv":"RCV000894054","title":"NM_014305.4(TGDS):c.983-8C>T AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227128,"stop":95227129,"reference":"C","alternative":"CA","vcv":"VCV001261515","referenceAssertions":[{"rcv":"RCV001674093","title":"NM_014305.4(TGDS):c.983-34dup AND not 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-{"release":"GRCh37","chromosome":"13","start":95227140,"stop":95227141,"reference":"AAG","alternative":"A","vcv":"VCV001228958","referenceAssertions":[{"rcv":"RCV001616589","title":"NM_014305.4(TGDS):c.983-35_983-34del AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95227340,"stop":95227340,"reference":"C","alternative":"T","vcv":"VCV001288190","referenceAssertions":[{"rcv":"RCV001707165","title":"NM_014305.4(TGDS):c.983-234G>A AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95228593,"stop":95228593,"reference":"A","alternative":"G","vcv":"VCV001575281","referenceAssertions":[{"rcv":"RCV002083442","title":"NM_014305.4(TGDS):c.957T>C (p.Pro319=) AND not 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-{"release":"GRCh37","chromosome":"13","start":95229675,"stop":95229675,"reference":"C","alternative":"G","vcv":"VCV002278206","referenceAssertions":[{"rcv":"RCV002822699","title":"NM_014305.4(TGDS):c.834G>C (p.Glu278Asp) AND Inborn genetic diseases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95229697,"stop":95229697,"reference":"A","alternative":"G","vcv":"VCV001617317","referenceAssertions":[{"rcv":"RCV002076513","title":"NM_014305.4(TGDS):c.826-14T>C AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} -{"release":"GRCh37","chromosome":"13","start":95229735,"stop":95229735,"reference":"A","alternative":"G","vcv":"VCV001260430","referenceAssertions":[{"rcv":"RCV001669248","title":"NM_014305.4(TGDS):c.826-52T>C AND not 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'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."},"type":"public definition"}}],"xrefs":[{"db":"MedGen","id":"C3661900"}]}],"type":"TYPE_DISEASE","id":"9460","contributesToAggregateClassification":true}],"dateLastEvaluated":"2023-10-05T00:00:00+00:00","dateCreated":"2023-07-08T00:00:00+00:00","mostRecentSubmission":"2024-05-01T00:00:00+00:00","numberOfSubmitters":2,"numberOfSubmissions":2}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95248366,"stop":95248366,"displayStart":95248366,"displayStop":95248366,"variantLength":1,"positionVcf":95248366,"referenceAlleleVcf":"G","alternateAlleleVcf":"A"},"hgncIds":["HGNC:20324"]} +{"accession":{"accession":"VCV000778479","version":8},"rcvs":[{"accession":{"accession":"RCV000959128","version":6},"title":"NM_014305.4(TGDS):c.12G>A (p.Ala4=) AND not provided"},{"accession":{"accession":"RCV003943091","version":1},"title":"NM_014305.4(TGDS):c.12G>A (p.Ala4=) AND TGDS-related condition"}],"name":"NM_014305.4(TGDS):c.12G>A (p.Ala4=)","variationType":"VARIATION_TYPE_SNV","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS","description":"Benign/Likely benign","conditions":[{"traits":[{"names":[{"value":"TGDS-related condition","type":"Preferred"}]}],"type":"TYPE_DISEASE","id":"91573","contributesToAggregateClassification":true},{"traits":[{"names":[{"value":"not provided","type":"Preferred","xrefs":[{"db":"Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre","id":"13DG0619"}]},{"value":"none provided","type":"Alternate"}],"attributes":[{"attribute":{"base":{"value":"The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."},"type":"public definition"}}],"xrefs":[{"db":"MedGen","id":"C3661900"}]}],"type":"TYPE_DISEASE","id":"9460","contributesToAggregateClassification":true}],"dateLastEvaluated":"2023-10-17T00:00:00+00:00","dateCreated":"2019-12-17T00:00:00+00:00","mostRecentSubmission":"2024-03-16T00:00:00+00:00","numberOfSubmitters":2,"numberOfSubmissions":2}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95248379,"stop":95248379,"displayStart":95248379,"displayStop":95248379,"variantLength":1,"positionVcf":95248379,"referenceAlleleVcf":"C","alternateAlleleVcf":"T"},"hgncIds":["HGNC:20324"]} +{"accession":{"accession":"VCV003044655","version":1},"rcvs":[{"accession":{"accession":"RCV003939865","version":1},"title":"NM_014305.4(TGDS):c.-10G>A AND TGDS-related condition"}],"name":"NM_014305.4(TGDS):c.-10G>A","variationType":"VARIATION_TYPE_SNV","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Likely benign","conditions":[{"traits":[{"names":[{"value":"TGDS-related condition","type":"Preferred"}]}],"type":"TYPE_DISEASE","id":"91573","contributesToAggregateClassification":true}],"dateLastEvaluated":"2023-12-20T00:00:00+00:00","dateCreated":"2024-03-17T00:00:00+00:00","mostRecentSubmission":"2024-03-16T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95248400,"stop":95248400,"displayStart":95248400,"displayStop":95248400,"variantLength":1,"positionVcf":95248400,"referenceAlleleVcf":"C","alternateAlleleVcf":"T"},"hgncIds":["HGNC:20324"]} +{"accession":{"accession":"VCV001255243","version":3},"rcvs":[{"accession":{"accession":"RCV001653352","version":2},"title":"NC_000013.11:g.94596312C>T AND not provided"}],"name":"NC_000013.11:g.94596312C>T","variationType":"VARIATION_TYPE_SNV","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Benign","conditions":[{"traits":[{"names":[{"value":"none provided","type":"Alternate"},{"value":"not provided","type":"Preferred","xrefs":[{"db":"Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre","id":"13DG0619"}]}],"attributes":[{"attribute":{"base":{"value":"The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."},"type":"public definition"}}],"xrefs":[{"db":"MedGen","id":"C3661900"}]}],"type":"TYPE_DISEASE","id":"9460","contributesToAggregateClassification":true}],"dateLastEvaluated":"2018-11-12T00:00:00+00:00","dateCreated":"2021-09-19T00:00:00+00:00","mostRecentSubmission":"2023-10-07T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95248566,"stop":95248566,"displayStart":95248566,"displayStop":95248566,"variantLength":1,"positionVcf":95248566,"referenceAlleleVcf":"C","alternateAlleleVcf":"T"},"hgncIds":["HGNC:20324"]} +{"accession":{"accession":"VCV001269376","version":2},"rcvs":[{"accession":{"accession":"RCV001681009","version":1},"title":"NC_000013.11:g.94596497C>T AND not provided"}],"name":"NC_000013.11:g.94596497C>T","variationType":"VARIATION_TYPE_SNV","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Benign","conditions":[{"traits":[{"names":[{"value":"not provided","type":"Preferred","xrefs":[{"db":"Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre","id":"13DG0619"}]},{"value":"none provided","type":"Alternate"}],"attributes":[{"attribute":{"base":{"value":"The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."},"type":"public definition"}}],"xrefs":[{"db":"MedGen","id":"C3661900"}]}],"type":"TYPE_DISEASE","id":"9460","contributesToAggregateClassification":true}],"dateLastEvaluated":"2021-05-22T00:00:00+00:00","dateCreated":"2021-09-24T00:00:00+00:00","mostRecentSubmission":"2023-10-07T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95248751,"stop":95248751,"displayStart":95248751,"displayStop":95248751,"variantLength":1,"positionVcf":95248751,"referenceAlleleVcf":"C","alternateAlleleVcf":"T"},"hgncIds":["HGNC:20324"]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_first.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_first.snap index ee234e9a..fdee8009 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_first.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_first.snap @@ -2,5 +2,4 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95227055,"stop":95227055,"reference":"A","alternative":"G","vcv":"VCV001309690","referenceAssertions":[{"rcv":"RCV001756758","title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} - +{"accession":{"accession":"VCV001309690","version":2},"rcvs":[{"accession":{"accession":"RCV001756758","version":2},"title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided"}],"name":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser)","variationType":"VARIATION_TYPE_SNV","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Uncertain significance","conditions":[{"traits":[{"names":[{"value":"none provided","type":"Alternate"},{"value":"not provided","type":"Preferred","xrefs":[{"db":"Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre","id":"13DG0619"}]}],"attributes":[{"attribute":{"base":{"value":"The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."},"type":"public definition"}}],"xrefs":[{"db":"MedGen","id":"C3661900"}]}],"type":"TYPE_DISEASE","id":"9460","contributesToAggregateClassification":true}],"dateLastEvaluated":"2019-11-13T00:00:00+00:00","dateCreated":"2021-11-06T00:00:00+00:00","mostRecentSubmission":"2023-03-04T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95227055,"stop":95227055,"displayStart":95227055,"displayStop":95227055,"variantLength":1,"positionVcf":95227055,"referenceAlleleVcf":"A","alternateAlleleVcf":"G"},"hgncIds":["HGNC:20324"]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_second.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_second.snap index 32decefe..1f8689b9 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_second.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_range_find_second.snap @@ -2,5 +2,4 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95227093,"stop":95227093,"reference":"T","alternative":"C","vcv":"VCV000792370","referenceAssertions":[{"rcv":"RCV000975465","title":"NM_014305.4(TGDS):c.996A>G (p.Arg332=) AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} - +{"accession":{"accession":"VCV000792370","version":3},"rcvs":[{"accession":{"accession":"RCV000975465","version":3},"title":"NM_014305.4(TGDS):c.996A>G (p.Arg332=) AND not provided"}],"name":"NM_014305.4(TGDS):c.996A>G (p.Arg332=)","variationType":"VARIATION_TYPE_SNV","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Likely benign","conditions":[{"traits":[{"names":[{"value":"not provided","type":"Preferred","xrefs":[{"db":"Developmental Genetics Unit, King Faisal Specialist Hospital & Research Centre","id":"13DG0619"}]},{"value":"none provided","type":"Alternate"}],"attributes":[{"attribute":{"base":{"value":"The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."},"type":"public definition"}}],"xrefs":[{"db":"MedGen","id":"CN517202"}]}],"type":"TYPE_DISEASE","id":"9460","contributesToAggregateClassification":true}],"dateLastEvaluated":"2018-10-10T00:00:00+00:00","dateCreated":"2019-12-17T00:00:00+00:00","mostRecentSubmission":"2019-12-17T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95227093,"stop":95227093,"displayStart":95227093,"displayStop":95227093,"variantLength":1,"positionVcf":95227093,"referenceAlleleVcf":"T","alternateAlleleVcf":"C"},"hgncIds":["HGNC:20324"]} diff --git a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_var_single.snap b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_var_single.snap index ee234e9a..fdee8009 100644 --- a/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_var_single.snap +++ b/src/clinvar_minimal/cli/snapshots/annonars__clinvar_minimal__cli__query__test__smoke_query_var_single.snap @@ -2,5 +2,4 @@ source: src/clinvar_minimal/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"13","start":95227055,"stop":95227055,"reference":"A","alternative":"G","vcv":"VCV001309690","referenceAssertions":[{"rcv":"RCV001756758","title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided","clinicalSignificance":"CLINICAL_SIGNIFICANCE_UNCERTAIN_SIGNIFICANCE","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER"}]} - +{"accession":{"accession":"VCV001309690","version":2},"rcvs":[{"accession":{"accession":"RCV001756758","version":2},"title":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser) AND not provided"}],"name":"NM_014305.4(TGDS):c.1034T>C (p.Leu345Ser)","variationType":"VARIATION_TYPE_SNV","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Uncertain significance","conditions":[{"traits":[{"names":[{"value":"none provided","type":"Alternate"},{"value":"not provided","type":"Preferred","xrefs":[{"db":"Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre","id":"13DG0619"}]}],"attributes":[{"attribute":{"base":{"value":"The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified."},"type":"public definition"}}],"xrefs":[{"db":"MedGen","id":"C3661900"}]}],"type":"TYPE_DISEASE","id":"9460","contributesToAggregateClassification":true}],"dateLastEvaluated":"2019-11-13T00:00:00+00:00","dateCreated":"2021-11-06T00:00:00+00:00","mostRecentSubmission":"2023-03-04T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_13","accession":"NC_000013.10","start":95227055,"stop":95227055,"displayStart":95227055,"displayStop":95227055,"variantLength":1,"positionVcf":95227055,"referenceAlleleVcf":"A","alternateAlleleVcf":"G"},"hgncIds":["HGNC:20324"]} diff --git a/src/clinvar_sv/cli/import.rs b/src/clinvar_sv/cli/import.rs index e01b68a2..d31c2d02 100644 --- a/src/clinvar_sv/cli/import.rs +++ b/src/clinvar_sv/cli/import.rs @@ -3,9 +3,9 @@ use std::{io::BufRead, sync::Arc}; use clap::Parser; -use prost::Message; +use prost::Message as _; -use crate::{clinvar_minimal, common}; +use crate::common; /// Command line arguments for `clinvar-sv import` sub command. #[derive(Parser, Debug, Clone)] @@ -57,7 +57,10 @@ fn jsonl_import( for line in reader.lines() { let line = line?; - let record = match serde_json::from_str::(&line) { + let vcv_record = match serde_json::from_str::< + crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord, + >(&line) + { Ok(record) => record, Err(e) => { tracing::warn!("skipping line because of error: {}", e); @@ -65,22 +68,16 @@ fn jsonl_import( } }; - let clinvar_minimal::cli::reading::Record { - rcv, - vcv, - title, - clinical_significance, - review_status, + let crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord { + accession, + rcvs: rcv_records, sequence_location, - variant_type, .. - } = record; - let clinical_significance: crate::pbs::clinvar::minimal::ClinicalSignificance = - clinical_significance.into(); - let review_status: crate::pbs::clinvar::minimal::ReviewStatus = review_status.into(); - let clinvar_minimal::cli::reading::SequenceLocation { - assembly, - chr, + } = vcv_record.clone(); + let accession = accession.expect("accession is required"); + let vcv = format!("{}.{}", accession.accession, accession.version); + let sequence_location = sequence_location.expect("sequence_location is required"); + let crate::pbs::clinvar_data::clinvar_public::location::SequenceLocation { start, stop, reference_allele_vcf, @@ -89,8 +86,8 @@ fn jsonl_import( inner_stop, outer_start, outer_stop, + .. } = sequence_location; - if let (Some(reference_allele_vcf), Some(alternate_allee_vcf)) = (reference_allele_vcf.as_ref(), alternate_allele_vcf.as_ref()) { @@ -98,9 +95,8 @@ fn jsonl_import( && alternate_allee_vcf.len() < args.min_var_size as usize { tracing::debug!( - "skipping line because of short REF/ALT: {}/{}: {}>{}", + "skipping line because of short REF/ALT: {}: {}>{}", &vcv, - &rcv, reference_allele_vcf, alternate_allee_vcf, ); @@ -108,97 +104,26 @@ fn jsonl_import( } } - let (start, stop, inner_start, inner_stop, outer_start, outer_stop) = - if let (Some(start), Some(stop)) = (start, stop) { - ( - start, - stop, - inner_start, - outer_start, - inner_stop, - outer_stop, - ) - } else if let (Some(inner_start_), Some(inner_stop_)) = (inner_start, inner_stop) { - ( - inner_start_, - inner_stop_, - inner_start, - outer_start, - inner_stop, - outer_stop, - ) - } else if let (Some(outer_start_), Some(outer_stop_)) = (outer_start, outer_stop) { - ( - outer_start_, - outer_stop_, - inner_start, - outer_start, - inner_stop, - outer_stop, - ) - } else { - tracing::warn!("skipping line because no start/stop: {}/{}", &vcv, &rcv,); - continue; - }; + if (start.is_none() || stop.is_none()) + && (inner_start.is_none() || inner_stop.is_none()) + && (outer_start.is_none() || outer_stop.is_none()) + { + tracing::warn!("skipping line because no start/stop: {}", &vcv,); + continue; + }; let key: Vec = vcv.clone().into(); - let data = db - .get_cf(&cf_data, key.clone()) - .map_err(|e| anyhow::anyhow!("problem querying database: {}", e)); - match data { - Err(e) => { - tracing::warn!("skipping line because of error: {}", e); - continue; - } - Ok(data) => { - let record = if let Some(data) = data { - let mut record = crate::pbs::clinvar::sv::Record::decode(&data[..])?; - record.reference_assertions.push( - crate::pbs::clinvar::minimal::ReferenceAssertion { - rcv: rcv.clone(), - title, - clinical_significance: clinical_significance.into(), - review_status: review_status.into(), - }, - ); - record - .reference_assertions - .sort_by_key(|a| (a.clinical_significance, a.review_status)); - record - } else { - crate::pbs::clinvar::sv::Record { - release: assembly, - chromosome: chr, - start, - stop, - reference: reference_allele_vcf, - alternative: alternate_allele_vcf, - vcv: vcv.clone(), - reference_assertions: vec![ - crate::pbs::clinvar::minimal::ReferenceAssertion { - rcv: rcv.clone(), - title, - clinical_significance: clinical_significance.into(), - review_status: review_status.into(), - }, - ], - inner_start, - inner_stop, - outer_start, - outer_stop, - variant_type: crate::pbs::clinvar::minimal::VariantType::from(variant_type) - as i32, - } - }; - let buf = record.encode_to_vec(); - db.put_cf(&cf_data, key, buf)?; - db.put_cf( - &cf_by_rcv, - rcv.clone().into_bytes(), - vcv.clone().into_bytes(), - )?; - } + let buf = vcv_record.encode_to_vec(); + db.put_cf(&cf_data, &key, &buf)?; + + for rcv_record in &rcv_records { + let accession = rcv_record + .accession + .as_ref() + .expect("rcv.accession is required"); + let rcv = format!("{}.{}", accession.accession, accession.version); + db.put_cf(&cf_by_rcv, rcv.as_bytes(), &key)?; } } diff --git a/src/clinvar_sv/cli/query.rs b/src/clinvar_sv/cli/query.rs index 5c6176b5..2f1d69a2 100644 --- a/src/clinvar_sv/cli/query.rs +++ b/src/clinvar_sv/cli/query.rs @@ -109,7 +109,7 @@ pub fn open_rocksdb_from_args( fn print_record( out_writer: &mut Box, output_format: common::cli::OutputFormat, - value: &crate::pbs::clinvar::sv::Record, + value: &crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord, ) -> Result<(), anyhow::Error> { match output_format { common::cli::OutputFormat::Jsonl => { @@ -126,7 +126,7 @@ pub fn query_for_accession( db: &rocksdb::DBWithThreadMode, cf_data: &Arc, cf_by_rcv: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { // Execute query. tracing::debug!("accession = {:?}", &accession); let vcv = if accession.starts_with("VCV") { @@ -145,8 +145,10 @@ pub fn query_for_accession( raw_value .map(|raw_value| { // Decode via prost. - crate::pbs::clinvar::sv::Record::decode(&mut std::io::Cursor::new(&raw_value)) - .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) + crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord::decode( + &mut std::io::Cursor::new(&raw_value), + ) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e)) }) .transpose() } @@ -164,9 +166,10 @@ fn print_all( iter.seek(b""); while iter.valid() { if let Some(raw_value) = iter.value() { - let record = - crate::pbs::clinvar::sv::Record::decode(&mut std::io::Cursor::new(&raw_value)) - .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; + let record = crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord::decode( + &mut std::io::Cursor::new(&raw_value), + ) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; print_record(out_writer, out_format, &record)?; iter.next(); } else { @@ -239,26 +242,67 @@ impl IntervalTrees { iter.seek(b""); while iter.valid() { if let Some(raw_value) = iter.value() { - let record = - crate::pbs::clinvar::sv::Record::decode(&mut std::io::Cursor::new(&raw_value)) - .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; + let record = crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord::decode( + &mut std::io::Cursor::new(&raw_value), + ) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; tracing::trace!("iterator at {:?} => {:?}", &iter.key(), &record); - let crate::pbs::clinvar::sv::Record { - chromosome, + let crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord { + accession, + sequence_location, + .. + } = record; + let accession = accession.expect("accession is required"); + let vcv = format!("{}.{}", accession.accession, accession.version); + let sequence_location = sequence_location.expect("sequence_location is required"); + let crate::pbs::clinvar_data::clinvar_public::location::SequenceLocation { + chr, start, stop, - vcv, + inner_start, + inner_stop, + outer_start, + outer_stop, .. - } = record; + } = sequence_location.clone(); + let chr_pb = crate::pbs::clinvar_data::clinvar_public::Chromosome::try_from(chr) + .map_err(|e| { + anyhow::anyhow!( + "problem converting chromosome {} to Chromosome: {}", + chr, + e + ) + })?; + + let (start, stop) = if let (Some(start), Some(stop)) = (start, stop) { + (start, stop) + } else if let (Some(inner_start), Some(inner_stop)) = (inner_start, inner_stop) { + (inner_start, inner_stop) + } else if let (Some(outer_start), Some(outer_stop)) = (outer_start, outer_stop) { + (outer_start, outer_stop) + } else { + tracing::warn!( + "skipping record without start/stop: {:?}, {:?}", + &vcv, + &sequence_location + ); + iter.next(); + continue; + }; let interval = (start as u64 - 1)..(stop as u64); - tracing::trace!("contig = {} / {:?} / {}", &chromosome, &interval, &vcv); + tracing::trace!( + "contig = {} / {:?} / {}", + &chr_pb.as_chr_name(), + &interval, + &vcv + ); result - .entry(chromosome.clone()) + .entry(chr_pb.as_chr_name()) .or_default() .insert(interval, vcv); - assert!(result.contains_key(&chromosome)); + assert!(result.contains_key(&chr_pb.as_chr_name())); iter.next(); } else { @@ -275,7 +319,8 @@ impl IntervalTrees { pub fn query( &self, range: &spdi::Range, - ) -> Result, anyhow::Error> { + ) -> Result, anyhow::Error> + { let contig = extract_chrom::from_range(range, Some(&self.meta.genome_release))?; let cf_data = self.db.cf_handle(&self.cf_data_name).ok_or_else(|| { anyhow::anyhow!("no column family with name {:?} found", &self.cf_data_name) @@ -285,10 +330,11 @@ impl IntervalTrees { if let Some(tree) = self.trees.get(&contig) { for entry in tree.find(&interval) { if let Some(raw_value) = self.db.get_cf(&cf_data, entry.data().as_bytes())? { - let record = crate::pbs::clinvar::sv::Record::decode( - &mut std::io::Cursor::new(&raw_value), - ) - .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; + let record = + crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord::decode( + &mut std::io::Cursor::new(&raw_value), + ) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; result.push(record); } } @@ -368,7 +414,7 @@ mod test { verbose: clap_verbosity_flag::Verbosity::new(1, 0), }; let args = Args { - path_rocksdb: String::from("tests/clinvar-sv/clinvar-sv-grch37.tsv.db"), + path_rocksdb: String::from("tests/clinvar-sv/clinvar-sv-grch37.db"), cf_name: String::from("clinvar_sv"), cf_name_by_rcv: String::from("clinvar_sv_by_rcv"), out_file: temp.join("out").to_string_lossy().to_string(), @@ -382,7 +428,7 @@ mod test { #[test] fn smoke_query_var_vcv() -> Result<(), anyhow::Error> { let (common, args, _temp) = args(ArgsQuery { - accession: Some("VCV000057688".into()), + accession: Some("VCV000057688.1".into()), ..Default::default() }); run(&common, &args)?; @@ -395,7 +441,7 @@ mod test { #[test] fn smoke_query_var_rcv() -> Result<(), anyhow::Error> { let (common, args, _temp) = args(ArgsQuery { - accession: Some("RCV000051426".into()), + accession: Some("RCV000051426.5".into()), ..Default::default() }); run(&common, &args)?; diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_all.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_all.snap index 27f79836..8fa40a6c 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_all.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_all.snap @@ -2,24 +2,23 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"X","start":155210040,"stop":155242832,"innerStart":155210040,"outerStart":155242832,"vcv":"VCV000057500","referenceAssertions":[{"rcv":"RCV000051210","title":"GRCh38/hg38 Xq28(chrX:155980375-156013167)x0 AND See cases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_BENIGN","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} -{"release":"GRCh37","chromosome":"7","start":64691936,"stop":64866073,"innerStart":64691936,"outerStart":64866073,"vcv":"VCV000057566","referenceAssertions":[{"rcv":"RCV000051294","title":"GRCh38/hg38 7q11.21(chr7:65231558-65401160)x1 AND See cases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_PATHOGENIC","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} -{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"innerStart":34150132,"outerStart":34182300,"vcv":"VCV000057627","referenceAssertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} -{"release":"GRCh37","chromosome":"X","start":73055208,"stop":73059460,"innerStart":73055208,"outerStart":73059460,"vcv":"VCV000057653","referenceAssertions":[{"rcv":"RCV000051388","title":"GRCh38/hg38 Xq13.2(chrX:73835373-73839625)x1 AND See cases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_PATHOGENIC","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} -{"release":"GRCh37","chromosome":"X","start":78605903,"stop":79090819,"innerStart":78605903,"outerStart":79090819,"vcv":"VCV000057654","referenceAssertions":[{"rcv":"RCV000051389","title":"GRCh38/hg38 Xq21.1(chrX:79350406-79835322)x0 AND See cases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_PATHOGENIC","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} -{"release":"GRCh37","chromosome":"X","start":89330088,"stop":89853974,"innerStart":89330088,"outerStart":89853974,"vcv":"VCV000057686","referenceAssertions":[{"rcv":"RCV000051424","title":"GRCh38/hg38 Xq21.31(chrX:90075089-90598975)x1 AND See cases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_PATHOGENIC","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} -{"release":"GRCh37","chromosome":"X","start":102885179,"stop":102967225,"innerStart":102885179,"outerStart":102967225,"vcv":"VCV000057688","referenceAssertions":[{"rcv":"RCV000051426","title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_PATHOGENIC","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} -{"release":"GRCh37","chromosome":"1","start":196757278,"stop":196796716,"innerStart":196757278,"outerStart":196796716,"vcv":"VCV000058538","referenceAssertions":[{"rcv":"RCV000052307","title":"GRCh38/hg38 1q31.3(chr1:196788148-196827586)x1 AND See cases","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} -{"release":"GRCh37","chromosome":"7","start":27194426,"stop":27461954,"innerStart":27194426,"outerStart":27461954,"vcv":"VCV000058544","referenceAssertions":[{"rcv":"RCV000052313","title":"GRCh38/hg38 7p15.2(chr7:27154807-27422335)x1 AND See 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-{"release":"GRCh37","chromosome":"X","start":8597747,"stop":8674356,"innerStart":8597747,"outerStart":8674356,"variantType":"VARIANT_TYPE_DELETION","vcv":"VCV000058567","referenceAssertions":[{"rcv":"RCV000052338","title":"GRCh38/hg38 Xp22.31(chrX:8629706-8706315)x3 AND See cases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_PATHOGENIC","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_CONFLICTING_INTERPRETATIONS"}]} -{"release":"GRCh37","chromosome":"X","start":28777940,"stop":29112528,"innerStart":28777940,"outerStart":29112528,"variantType":"VARIANT_TYPE_DELETION","vcv":"VCV000058611","referenceAssertions":[{"rcv":"RCV000052386","title":"GRCh38/hg38 Xp21.3(chrX:28759823-29094411)x2 AND See cases","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} 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+{"accession":{"accession":"VCV000144128","version":1},"rcvs":[{"accession":{"accession":"RCV000052335","version":4},"title":"GRCh38/hg38 Xp22.31(chrX:8627004-8736337)x3 AND See cases"}],"name":"GRCh38/hg38 Xp22.31(chrX:8627004-8736337)x3","variationType":"VARIATION_TYPE_COPY_NUMBER_GAIN","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Uncertain significance","conditions":[{"traits":[{"names":[{"value":"See 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b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_exact.snap @@ -2,5 +2,4 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"innerStart":34150132,"outerStart":34182300,"vcv":"VCV000057627","referenceAssertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} - +{"accession":{"accession":"VCV000057627","version":1},"rcvs":[{"accession":{"accession":"RCV000051361","version":6},"title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases"}],"name":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1","variationType":"VARIATION_TYPE_COPY_NUMBER_LOSS","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Pathogenic","conditions":[{"traits":[{"names":[{"value":"See cases","type":"Preferred"}]}],"type":"TYPE_PHENOTYPE_INSTRUCTION","id":"16994","contributesToAggregateClassification":true}],"dateLastEvaluated":"2011-08-12T00:00:00+00:00","dateCreated":"2015-06-29T00:00:00+00:00","mostRecentSubmission":"2015-06-29T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_22","accession":"NC_000022.10","innerStart":34150132,"innerStop":34182300,"displayStart":34150132,"displayStop":34182300,"variantLength":32169},"hgncIds":["HGNC:6511"]} diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_no_overlap.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_no_overlap.snap index 4787fbcc..5efe00ae 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_no_overlap.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_no_overlap.snap @@ -2,5 +2,4 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"innerStart":34150132,"outerStart":34182300,"vcv":"VCV000057627","referenceAssertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} - +{"accession":{"accession":"VCV000057627","version":1},"rcvs":[{"accession":{"accession":"RCV000051361","version":6},"title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases"}],"name":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1","variationType":"VARIATION_TYPE_COPY_NUMBER_LOSS","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Pathogenic","conditions":[{"traits":[{"names":[{"value":"See cases","type":"Preferred"}]}],"type":"TYPE_PHENOTYPE_INSTRUCTION","id":"16994","contributesToAggregateClassification":true}],"dateLastEvaluated":"2011-08-12T00:00:00+00:00","dateCreated":"2015-06-29T00:00:00+00:00","mostRecentSubmission":"2015-06-29T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_22","accession":"NC_000022.10","innerStart":34150132,"innerStop":34182300,"displayStart":34150132,"displayStop":34182300,"variantLength":32169},"hgncIds":["HGNC:6511"]} diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_overlap.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_overlap.snap index 4787fbcc..5efe00ae 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_overlap.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_range_overlap.snap @@ -2,5 +2,4 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"22","start":34150132,"stop":34182300,"innerStart":34150132,"outerStart":34182300,"vcv":"VCV000057627","referenceAssertions":[{"rcv":"RCV000051361","title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} - +{"accession":{"accession":"VCV000057627","version":1},"rcvs":[{"accession":{"accession":"RCV000051361","version":6},"title":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1 AND See cases"}],"name":"GRCh38/hg38 22q12.3(chr22:33754145-33786313)x1","variationType":"VARIATION_TYPE_COPY_NUMBER_LOSS","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Pathogenic","conditions":[{"traits":[{"names":[{"value":"See cases","type":"Preferred"}]}],"type":"TYPE_PHENOTYPE_INSTRUCTION","id":"16994","contributesToAggregateClassification":true}],"dateLastEvaluated":"2011-08-12T00:00:00+00:00","dateCreated":"2015-06-29T00:00:00+00:00","mostRecentSubmission":"2015-06-29T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_22","accession":"NC_000022.10","innerStart":34150132,"innerStop":34182300,"displayStart":34150132,"displayStop":34182300,"variantLength":32169},"hgncIds":["HGNC:6511"]} diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_rcv.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_rcv.snap index 0e1e97ab..82a5a7d8 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_rcv.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_rcv.snap @@ -2,5 +2,4 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"X","start":102885179,"stop":102967225,"innerStart":102885179,"outerStart":102967225,"vcv":"VCV000057688","referenceAssertions":[{"rcv":"RCV000051426","title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_PATHOGENIC","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} - +{"accession":{"accession":"VCV000057688","version":1},"rcvs":[{"accession":{"accession":"RCV000051426","version":5},"title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases"}],"name":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1","variationType":"VARIATION_TYPE_COPY_NUMBER_LOSS","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Uncertain significance","conditions":[{"traits":[{"names":[{"value":"See cases","type":"Preferred"}]}],"type":"TYPE_PHENOTYPE_INSTRUCTION","id":"16994","contributesToAggregateClassification":true}],"dateLastEvaluated":"2011-08-12T00:00:00+00:00","dateCreated":"2015-06-28T00:00:00+00:00","mostRecentSubmission":"2015-06-28T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_X","accession":"NC_000023.10","innerStart":102885179,"innerStop":102967225,"displayStart":102885179,"displayStop":102967225,"variantLength":82047},"hgncIds":["HGNC:16849","HGNC:27991","HGNC:11616","HGNC:28601"]} diff --git a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_vcv.snap b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_vcv.snap index 0e1e97ab..82a5a7d8 100644 --- a/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_vcv.snap +++ b/src/clinvar_sv/cli/snapshots/annonars__clinvar_sv__cli__query__test__smoke_query_var_vcv.snap @@ -2,5 +2,4 @@ source: src/clinvar_sv/cli/query.rs expression: "&out_data" --- -{"release":"GRCh37","chromosome":"X","start":102885179,"stop":102967225,"innerStart":102885179,"outerStart":102967225,"vcv":"VCV000057688","referenceAssertions":[{"rcv":"RCV000051426","title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases","clinicalSignificance":"CLINICAL_SIGNIFICANCE_LIKELY_PATHOGENIC","reviewStatus":"REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS"}]} - +{"accession":{"accession":"VCV000057688","version":1},"rcvs":[{"accession":{"accession":"RCV000051426","version":5},"title":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1 AND See cases"}],"name":"GRCh38/hg38 Xq22.2(chrX:103630251-103712297)x1","variationType":"VARIATION_TYPE_COPY_NUMBER_LOSS","classifications":{"germlineClassification":{"reviewStatus":"AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER","description":"Uncertain significance","conditions":[{"traits":[{"names":[{"value":"See cases","type":"Preferred"}]}],"type":"TYPE_PHENOTYPE_INSTRUCTION","id":"16994","contributesToAggregateClassification":true}],"dateLastEvaluated":"2011-08-12T00:00:00+00:00","dateCreated":"2015-06-28T00:00:00+00:00","mostRecentSubmission":"2015-06-28T00:00:00+00:00","numberOfSubmitters":1,"numberOfSubmissions":1}},"sequenceLocation":{"assembly":"GRCh37","chr":"CHROMOSOME_X","accession":"NC_000023.10","innerStart":102885179,"innerStop":102967225,"displayStart":102885179,"displayStop":102967225,"variantLength":82047},"hgncIds":["HGNC:16849","HGNC:27991","HGNC:11616","HGNC:28601"]} diff --git a/src/pbs/clinvar.rs b/src/pbs/clinvar.rs index ebdc58b1..294253d9 100644 --- a/src/pbs/clinvar.rs +++ b/src/pbs/clinvar.rs @@ -1,20 +1,20 @@ //! Code generate for protobufs by `prost-build`. /// Code generate for protobufs by `prost-build`. -pub mod minimal { - include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.minimal.rs")); +pub mod per_gene { + include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.per_gene.rs")); include!(concat!( env!("OUT_DIR"), - "/annonars.clinvar.minimal.serde.rs" + "/annonars.clinvar.per_gene.serde.rs" )); } /// Code generate for protobufs by `prost-build`. -pub mod per_gene { - include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.per_gene.rs")); +pub mod minimal { + include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.minimal.rs")); include!(concat!( env!("OUT_DIR"), - "/annonars.clinvar.per_gene.serde.rs" + "/annonars.clinvar.minimal.serde.rs" )); } @@ -23,21 +23,55 @@ pub mod sv { include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.sv.rs")); include!(concat!(env!("OUT_DIR"), "/annonars.clinvar.sv.serde.rs")); - impl From for bio::bio_types::genome::Interval { - fn from(val: Record) -> Self { - bio::bio_types::genome::Interval::new( - val.chromosome, - (val.start as u64 - 1)..(val.stop as u64), - ) + // TODO: TryFrom would be more appropriate + impl From + for bio::bio_types::genome::Interval + { + fn from(val: crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord) -> Self { + let crate::pbs::clinvar_data::clinvar_public::location::SequenceLocation { + chr, + start, + stop, + .. + } = val + .sequence_location + .as_ref() + .expect("missing sequence_location"); + let start = start.expect("missing start"); + let stop = stop.expect("missing stop"); + match crate::pbs::clinvar_data::clinvar_public::Chromosome::try_from(*chr) { + Ok(chr) => bio::bio_types::genome::Interval::new( + chr.as_chr_name(), + (start as u64 - 1)..(stop as u64), + ), + Err(e) => panic!("problem converting chromosome {} to Chromosome: {}", chr, e), + } } } - impl From<&Record> for bio::bio_types::genome::Interval { - fn from(val: &Record) -> Self { - bio::bio_types::genome::Interval::new( - val.chromosome.clone(), - (val.start as u64 - 1)..(val.stop as u64), - ) + // TODO: TryFrom would be more appropriate + impl From<&crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord> + for bio::bio_types::genome::Interval + { + fn from(val: &crate::pbs::clinvar_data::extracted_vars::ExtractedVcvRecord) -> Self { + let crate::pbs::clinvar_data::clinvar_public::location::SequenceLocation { + chr, + start, + stop, + .. + } = val + .sequence_location + .as_ref() + .expect("missing sequence_location"); + let start = start.expect("missing start"); + let stop = stop.expect("missing stop"); + match crate::pbs::clinvar_data::clinvar_public::Chromosome::try_from(*chr) { + Ok(chr) => bio::bio_types::genome::Interval::new( + chr.as_chr_name(), + (start as u64 - 1)..(stop as u64), + ), + Err(e) => panic!("problem converting chromosome {} to Chromosome: {}", chr, e), + } } } } diff --git a/src/pbs/clinvar_data.rs b/src/pbs/clinvar_data.rs index acab82a2..46a4956c 100644 --- a/src/pbs/clinvar_data.rs +++ b/src/pbs/clinvar_data.rs @@ -22,6 +22,13 @@ pub mod clinvar_public { env!("OUT_DIR"), "/annonars.clinvar_data.clinvar_public.serde.rs" )); + + impl Chromosome { + /// Return the chromosome name, e.g., "1", ..., "22", "X", "Y", "MT", "PAR", "Un". + pub fn as_chr_name(&self) -> String { + self.as_str_name().replace("CHROMOSOME_", "") + } + } } /// Code generated for protobufs by `prost-build`. @@ -34,6 +41,25 @@ pub mod extracted_vars { env!("OUT_DIR"), "/annonars.clinvar_data.extracted_vars.serde.rs" )); + + impl std::fmt::Display for VariationType { + fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { + write!( + f, + "{}", + serde_json::to_string(&self).map_err(|_| std::fmt::Error)? + ) + } + } + + impl std::str::FromStr for VariationType { + type Err = anyhow::Error; + + fn from_str(s: &str) -> Result { + serde_json::from_str(s) + .map_err(|e| anyhow::anyhow!("problem parsing VariationType: {}", e)) + } + } } /// Code generated for protobufs by `prost-build`. diff --git a/src/server/actix_server/annos_range.rs b/src/server/actix_server/annos_range.rs index e59b4276..74d46973 100644 --- a/src/server/actix_server/annos_range.rs +++ b/src/server/actix_server/annos_range.rs @@ -97,7 +97,7 @@ async fn handle( data.annos[genome_release][anno_db] .as_ref() .map(|db| { - fetch_pos_protobuf::( + fetch_pos_protobuf::( db, anno_db.cf_name(), query.start_pos(), diff --git a/src/server/actix_server/annos_variant.rs b/src/server/actix_server/annos_variant.rs index 3b9f974b..c632371e 100644 --- a/src/server/actix_server/annos_variant.rs +++ b/src/server/actix_server/annos_variant.rs @@ -92,7 +92,7 @@ async fn handle( data.annos[genome_release][anno_db] .as_ref() .map(|db| { - fetch_var_protobuf::( + fetch_var_protobuf::( db, anno_db.cf_name(), query.clone().into_inner().into(), diff --git a/src/server/actix_server/clinvar_sv.rs b/src/server/actix_server/clinvar_sv.rs index 1787056b..26fa45d3 100644 --- a/src/server/actix_server/clinvar_sv.rs +++ b/src/server/actix_server/clinvar_sv.rs @@ -11,87 +11,13 @@ use crate::common::{cli::GenomeRelease, spdi}; use super::error::CustomError; use serde_with::{formats::CommaSeparator, StringWithSeparator}; -use crate::pbs::clinvar::{ - minimal::VariantType as PbVariantType, - sv::{PageInfo, ResponsePage, ResponseRecord}, -}; +use crate::pbs::clinvar_data::extracted_vars::VariationType; /// The default page size to use. const DEFAULT_PAGE_SIZE: u32 = 100; /// The default minimal overlap. const DEFAULT_MIN_OVERLAP: f64 = 0.5; -/// Enumeration for `Request::variant_type`. -/// -/// We use the prefixed `SCREAMING_SNAKE_CASE` for consistency with the JSON -/// serialized protobufs. -#[serde_with::serde_as] -#[derive( - serde_with::SerializeDisplay, - serde_with::DeserializeFromStr, - Debug, - Clone, - Copy, - PartialEq, - Eq, - PartialOrd, - Ord, -)] -enum VariantType { - Unknown, - Deletion, - Duplication, - Indel, - Insertion, - Inversion, - Snv, -} - -impl std::fmt::Display for VariantType { - fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { - match self { - VariantType::Unknown => write!(f, "VARIANT_TYPE_UNKNOWN"), - VariantType::Deletion => write!(f, "VARIANT_TYPE_DELETION"), - VariantType::Duplication => write!(f, "VARIANT_TYPE_DUPLICATION"), - VariantType::Indel => write!(f, "VARIANT_TYPE_INDEL"), - VariantType::Insertion => write!(f, "VARIANT_TYPE_INSERTION"), - VariantType::Inversion => write!(f, "VARIANT_TYPE_INVERSION"), - VariantType::Snv => write!(f, "VARIANT_TYPE_SNV"), - } - } -} - -impl std::str::FromStr for VariantType { - type Err = anyhow::Error; - - fn from_str(s: &str) -> Result { - match s { - "VARIANT_TYPE_UNKNOWN" => Ok(VariantType::Unknown), - "VARIANT_TYPE_DELETION" => Ok(VariantType::Deletion), - "VARIANT_TYPE_DUPLICATION" => Ok(VariantType::Duplication), - "VARIANT_TYPE_INDEL" => Ok(VariantType::Indel), - "VARIANT_TYPE_INSERTION" => Ok(VariantType::Insertion), - "VARIANT_TYPE_INVERSION" => Ok(VariantType::Inversion), - "VARIANT_TYPE_SNV" => Ok(VariantType::Snv), - _ => Err(anyhow::anyhow!("unknown variant type: {}", s)), - } - } -} - -impl From for PbVariantType { - fn from(val: VariantType) -> Self { - match val { - VariantType::Unknown => PbVariantType::Unknown, - VariantType::Deletion => PbVariantType::Deletion, - VariantType::Duplication => PbVariantType::Duplication, - VariantType::Indel => PbVariantType::Indel, - VariantType::Insertion => PbVariantType::Insertion, - VariantType::Inversion => PbVariantType::Inversion, - VariantType::Snv => PbVariantType::Snv, - } - } -} - /// Parameters for `handle()`. /// /// We use `camelCase` for exposition on the REST API and consistency with @@ -111,8 +37,8 @@ struct Request { /// 1-based stop postion. pub stop: u32, /// Optionally, the variant types. - #[serde_as(as = "Option>")] - pub variant_type: Option>, + #[serde_as(as = "Option>")] + pub variation_types: Option>, /// Optionally, minimal overlap. pub min_overlap: Option, /// Optional 1-based page number. @@ -134,7 +60,13 @@ where let len_lhs = lhs.end - lhs.start; let len_rhs = rhs.end - rhs.start; let len_ovl = std::cmp::min(lhs.end, rhs.end) - std::cmp::max(lhs.start, rhs.start); - (Into::::into(len_ovl)) / Into::::into(len_lhs + len_rhs) + let res_lhs = Into::::into(len_ovl) / Into::::into(len_lhs); + let res_rhs = Into::::into(len_ovl) / Into::::into(len_rhs); + if res_lhs < res_rhs { + res_lhs + } else { + res_rhs + } } /// Query for annotations for one variant. @@ -178,33 +110,52 @@ async fn handle( )) })?; // Filter the records. - let variant_types = query - .variant_type + let variation_types = query + .variation_types .as_ref() - .map(|vs| { - vs.iter() - .map(|v| PbVariantType::from(*v) as i32) - .collect::>() - }) + .map(|vs| vs.iter().map(|v| *v as i32).collect::>()) .unwrap_or_default(); let records = { let mut records = records .into_iter() - .map(|record| { - let overlap = reciprocal_overlap( - &((query.start - 1)..query.stop), - &((record.start - 1)..record.stop), - ); - ResponseRecord { + .filter_map(|record| { + let crate::pbs::clinvar_data::clinvar_public::location::SequenceLocation { + start, + stop, + inner_start, + inner_stop, + outer_start, + outer_stop, + .. + } = record + .sequence_location + .clone() + .expect("missing sequence_location"); + let (start, stop) = if let (Some(start), Some(stop)) = (start, stop) { + (start, stop) + } else if let (Some(inner_start), Some(inner_stop)) = (inner_start, inner_stop) { + (inner_start, inner_stop) + } else if let (Some(outer_start), Some(outer_stop)) = (outer_start, outer_stop) { + (outer_start, outer_stop) + } else { + let accession = record.accession.clone().expect("missing accession"); + let vcv = format!("{}.{}", &accession.accession, &accession.version); + tracing::warn!("skipping record because no start/stop: {}", &vcv); + return None; + }; + + let overlap = + reciprocal_overlap(&((query.start - 1)..query.stop), &((start - 1)..stop)); + Some(crate::pbs::clinvar::sv::ResponseRecord { record: Some(record), overlap, - } + }) }) .filter(|record| { // filter by variant type if specified - if !variant_types.is_empty() { - return variant_types - .contains(&record.record.as_ref().expect("no record").variant_type); + if !variation_types.is_empty() { + return variation_types + .contains(&record.record.as_ref().expect("no record").variation_type); } // filter by overlap if specified let min_overlap = query.min_overlap.unwrap_or(DEFAULT_MIN_OVERLAP); @@ -226,14 +177,14 @@ async fn handle( let end = std::cmp::min(begin as u32 + per_page, records.len() as u32) as usize; let records = records[begin..end].to_vec(); - let page_info = PageInfo { + let page_info = crate::pbs::clinvar::sv::PageInfo { total: records.len() as u32, per_page, current_page, total_pages, }; - Ok(Json(ResponsePage { + Ok(Json(crate::pbs::clinvar::sv::ResponsePage { records, page_info: Some(page_info), })) diff --git a/tests/clinvar-minimal/bootstrap.sh b/tests/clinvar-minimal/bootstrap.sh index fb473e9e..8d09e2a5 100644 --- a/tests/clinvar-minimal/bootstrap.sh +++ b/tests/clinvar-minimal/bootstrap.sh @@ -6,20 +6,18 @@ set -x export TMPDIR=$(mktemp -d) trap "rm -rf $TMPDIR" EXIT -base=https://github.com/varfish-org/clinvar-data-jsonl/releases/download/clinvar-weekly-20231015 -wget -O $TMPDIR/clinvar-data-extract-vars-20231015+0.12.0.tar.gz \ - $base/clinvar-data-extract-vars-20231015+0.12.0.tar.gz -tar -C $TMPDIR -xf $TMPDIR/clinvar-data-extract-vars-20231015+0.12.0.tar.gz +base=https://github.com/varfish-org/clinvar-data-jsonl/releases/download/clinvar-weekly-20240528 +wget -O $TMPDIR/clinvar-data-extract-vars-20240528+0.15.5.tar.gz \ + $base/clinvar-data-extract-vars-20240528+0.15.5.tar.gz +tar -C $TMPDIR -xf $TMPDIR/clinvar-data-extract-vars-20240528+0.15.5.tar.gz set +o pipefail -zcat $TMPDIR/clinvar-data-extract-vars-20231015+0.12.0/clinvar-variants-grch37-seqvars.jsonl.gz \ -| egrep "pathogenic|benign|uncertain" \ -| grep -w HGNC:20324 \ -> $TMPDIR/clinvar-variants-grch37-seqvars.jsonl +zgrep -w HGNC:20324 $TMPDIR/clinvar-data-extract-vars-20240528+0.15.5/clinvar-variants-grch37-seqvars.jsonl.gz \ +> tests/clinvar-minimal/clinvar-seqvars-grch37-tgds.jsonl set -o pipefail -rm -rf tests/clinvar-minimal/clinvar-seqvars-grch37-tgds.tsv.db +rm -rf tests/clinvar-minimal/clinvar-seqvars-grch37-tgds.db cargo run --all-features -- \ clinvar-minimal import -vvv \ --genome-release grch37 \ - --path-in-jsonl $TMPDIR/clinvar-variants-grch37-seqvars.jsonl \ - --path-out-rocksdb tests/clinvar-minimal/clinvar-seqvars-grch37-tgds.tsv.db + --path-in-jsonl tests/clinvar-minimal/clinvar-seqvars-grch37-tgds.jsonl \ + --path-out-rocksdb tests/clinvar-minimal/clinvar-seqvars-grch37-tgds.db diff --git a/tests/clinvar-minimal/clinvar-seqvars-grch37-flagged.jsonl b/tests/clinvar-minimal/clinvar-seqvars-grch37-flagged.jsonl index 4c90d7e3..a2027d9a 100644 --- a/tests/clinvar-minimal/clinvar-seqvars-grch37-flagged.jsonl +++ b/tests/clinvar-minimal/clinvar-seqvars-grch37-flagged.jsonl @@ -1,10 +1,10 @@ -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000002453", "version": 16, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2013-04-04"}, "record_status": "current", "clinical_significance": {"review_status": "no assertion criteria provided", "description": "pathogenic", "date_last_evaluated": "2020-09-16"}, "assertion": "variation to disease", "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}, {"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "not provided"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "For discussion of the cys419-to-phe (C419F) mutation in the USH2A gene that was found in compound heterozygous state in patients with Usher syndrome type IIa (USH2A; 276901) by van Wijk et al. (2004), see 608400.0007."}, "citations": [{"ids": [{"source": "PubMed", "value": "15015129"}], "type": "general"}]}]}, {"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}, {"sample": {"origin": "inherited", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}]}, {"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}]}, {"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "acc": "VCV000002359", "version": 49, "measures": [{"type": "single nucleotide variant", "names": [{"value": {"type": "Preferred", "value": "NM_206933.4(USH2A):c.1256G>T (p.Cys419Phe)"}}], "canonical_spdi": "NC_000001.11:216324239:C:A", "attributes": [{"type": "HGVS, coding, RefSeq", "value": "NM_007123.6:c.1256G>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_206933.4:c.1256G>T"}, {"type": "HGVS, genomic, RefSeqGene", "value": "NG_009497.2:g.104209G>T"}, {"type": "HGVS, genomic, top level", "value": "NC_000001.11:g.216324240C>A", "integer_value": 38}, {"type": "HGVS, genomic, top level, previous", "value": "NC_000001.10:g.216497582C>A", "integer_value": 37}, {"type": "HGVS, incomplete", "value": "c.1256G>T"}, {"type": "HGVS, previous", "value": "NM_007123.5:c.1256G>T"}, {"type": "HGVS, previous", "value": "NM_206933.2:c.1256G>T"}, {"type": "HGVS, previous", "value": "NM_206933.3:c.1256G>T"}, {"type": "HGVS, previous", "value": "NG_009497.1:g.104157G>T"}, {"type": "HGVS, protein", "value": "O75445:p.Cys419Phe"}, {"type": "HGVS, protein, RefSeq", "value": "NP_009054.5:p.Cys419Phe"}, {"type": "HGVS, protein, RefSeq", "value": "NP_009054.6:p.Cys419Phe"}, {"type": "HGVS, protein, RefSeq", "value": "NP_996816.3:p.Cys419Phe"}, {"type": "Location", "value": "NM_206933.2:exon 7"}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_007123.6:c.1256G>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_206933.4:c.1256G>T"}]}, {"type": "ProteinChange1LetterCode", "value": "C419F"}, {"type": "ProteinChange3LetterCode", "value": "CYS419PHE"}], "cytogenic_locations": ["1q41"], "sequence_locations": [{"assembly": "GRCh38", "chr": "1", "accession": "NC_000001.11", "start": 216324240, "stop": 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"value": "NM_000271.5(NPC1):c.3019C>G (p.Pro1007Ala)"}}], "attributes": [{"type": "SubmitterVariantId", "value": "GDX:45061"}], "xrefs": [{"db": "ClinGen", "id": "CA340032"}], "id": 2966}, "traits": {"type": "Disease", "traits": [{"type": "Disease", "names": [{"value": {"type": "Preferred", "value": "Niemann-Pick disease, type C1"}, "xrefs": [{"db": "MONDO", "id": "MONDO:0009757"}]}, {"value": {"type": "Alternate", "value": "NIEMANN-PICK DISEASE WITHOUT SPHINGOMYELINASE DEFICIENCY"}, "xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}, {"value": {"type": "Alternate", "value": "Niemann-Pick disease with cholesterol esterification block"}}, {"value": {"type": "Alternate", "value": "Niemann-Pick disease, chronic neuronopathic form"}}, {"value": {"type": "Alternate", "value": "Neurovisceral storage disease with vertical supranuclear ophthalmoplegia"}}, {"value": {"type": "Alternate", "value": "NIEMANN-PICK DISEASE, VARIANT TYPE C1"}, "xrefs": [{"db": "OMIM", "id": "607623.0011", "type": "Allelic variant"}, {"db": "OMIM", "id": "607623.0012", "type": "Allelic variant"}]}], "symbols": [{"value": {"type": "Alternate", "value": "NPC1"}, "xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}], "attributes": [{"value": {"type": "public definition", "value": "Niemann-Pick disease type C (NPC) is a slowly progressive lysosomal disorder whose principal manifestations are age dependent. The manifestations in the perinatal period and infancy are predominantly visceral, with hepatosplenomegaly, jaundice, and (in some instances) pulmonary infiltrates. From late infancy onward, the presentation is dominated by neurologic manifestations. The youngest children may present with hypotonia and developmental delay, with the subsequent emergence of ataxia, dysarthria, dysphagia, and, in some individuals, epileptic seizures, dystonia, and gelastic cataplexy. Although cognitive impairment may be subtle at first, it eventually becomes apparent that affected individuals have a progressive dementia. Older teenagers and young adults may present predominantly with apparent early-onset dementia or psychiatric manifestations; however, careful examination usually identifies typical neurologic signs."}, "xrefs": [{"db": "GeneReviews", "id": "NBK1296"}]}, {"value": {"type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "7207"}]}], "citations": [{"ids": [{"source": "PubMed", "value": "20301473"}, {"source": "BookShelf", "value": "NBK1296"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "MONDO", "id": "MONDO:0009757"}, {"db": "MedGen", "id": "C3179455"}, {"db": "Orphanet", "id": "646"}, {"db": "OMIM", "id": "257220", "type": "MIM"}]}], "id": 753}, "date_created": "2013-04-04", "date_last_updated": "2023-12-09", "id": 60603}, "record_status": "current", "title": "NM_000271.5(NPC1):c.3019C>G (p.Pro1007Ala) AND Niemann-Pick disease, type C1", "clinvar_assertions": [{"id": 23258, "submission_id": {"local_key": "607623.0012_NIEMANN-PICK DISEASE, VARIANT TYPE C1", "submitter": "OMIM", "title": "NPC1, PRO1007ALA_NIEMANN-PICK DISEASE, VARIANT TYPE C1", "submitter_date": "2016-09-19"}, "clinvar_accession": {"acc": "SCV000023258", "version": 3, "type": "SCV", "date_updated": "2015-10-11", "date_created": "2013-04-04", "org_id": "3", "org_type": "primary", "org_category": "resource"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion criteria provided", "descriptions": ["pathogenic"], "date_last_evaluated": "2001-06-01"}], "external_ids": [{"db": "OMIM", "id": "607623.0012", "type": "Allelic variant"}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human"}, "affected_status": "not provided"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "For discussion of the pro1007-to-ala (P1007A) mutation in the NPC1 gene that was found in compound heterozygous state in patients with variant Niemann-Pick disease type C1 (257220) by Sun et al. (2001), see 607623.0011."}, "citations": [{"ids": [{"source": "PubMed", "value": "11349231"}]}], "xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}, {"attribute": {"type": "Description", "value": "In 3 families with variant Niemann-Pick disease type C1, Millat et al. (2001) found compound heterozygosity for the 2 most common alleles of the NPC1 gene, I1061T (607623.0010) and P1007A. Compound heterozygosity of these 2 alleles resulted in the juvenile onset of symptoms and a significantly slower progression of the disease than in homozygous I1061T patients. P1007A combined with the nonsense mutation in 1 patient studied by Millat et al. (2001) resulted in the late-infantile neurologic form."}, "citations": [{"ids": [{"source": "PubMed", "value": "11333381"}]}]}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "names": [{"value": {"type": "Preferred", "value": "NPC1, PRO1007ALA"}}], "attributes": [{"type": "NonHGVS", "value": "PRO1007ALA"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}], "xrefs": [{"db": "OMIM", "id": "607623.0012", "type": "Allelic variant"}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "NIEMANN-PICK DISEASE, VARIANT TYPE C1"}}]}]}}, {"id": 40575, "submission_id": {"local_key": "NM_000271.3:c.3019C>G_NBK1296", "submitter": "GeneReviews", "title": "NM_000271.3:c.3019C>G and Niemann-Pick Disease Type C", "submitter_date": "2013-03-26"}, "clinvar_accession": {"acc": "SCV000040575", "version": 3, "type": "SCV", "date_updated": "2022-10-01", "date_created": "2013-04-04", "org_id": "500062", "org_type": "primary", "org_category": "resource"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion provided", "descriptions": ["not provided"], "citations": [{"ids": [{"source": "PubMed", "value": "11333381"}], "type": "general"}, {"ids": [{"source": "PubMed", "value": "11349231"}], "type": "general"}, {"ids": [{"source": "PubMed", "value": "16098014"}], "type": "general"}, {"ids": [{"source": "PubMed", "value": "20301473"}], "type": "general"}, {"ids": [{"source": "BookShelf", "value": "NBK1296"}], "type": "general"}]}], "external_ids": [{"db": "GeneReviews", "id": "NBK1296"}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human"}, "affected_status": "not provided"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.3:c.3019C>G"}], "xrefs": [{"db": "dbSNP", "id": "80358257"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "MedGen", "id": "C3179455", "type": "CUI"}]}]}}, {"id": 721371, "submission_id": {"local_key": "650433", "submitter": "Illumina Laboratory Services, Illumina", "submitted_assembly": "GRCh37", "submitter_date": "2019-02-01"}, "clinvar_accession": {"acc": "SCV000407850", "version": 3, "type": "SCV", "date_updated": "2019-05-24", "date_created": "2016-12-06", "org_id": "504895", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "26666848"}]}, {"ids": [{"source": "PubMed", "value": "12401890"}]}, {"ids": [{"source": "PubMed", "value": "11479732"}]}, {"ids": [{"source": "PubMed", "value": "25349751"}]}, {"ids": [{"source": "PubMed", "value": "10521290"}]}, {"ids": [{"source": "PubMed", "value": "11349231"}]}, {"ids": [{"source": "PubMed", "value": "11333381"}]}, {"ids": [{"source": "PubMed", "value": "11754101"}]}, {"ids": [{"source": "PubMed", "value": "25425405"}]}, {"ids": [{"source": "PubMed", "value": "25236789"}]}, {"ids": [{"source": "PubMed", "value": "16098014"}]}], "comments": [{"text": "The NPC1 gene is one of two genes in which variants are known to cause Niemann-Pick disease type C. The NPC1 c.3019C>G (p.Pro1007Ala) variant is widely reported as a pathogenic variant and is the second most common pathogenic allele in Western Europe and the US (Patterson et al. 2000). Across a selection of the available literature, the p.Pro1007Ala variant has been identified in at least 44 Niemann-Pick disease type C patients including eight in a homozygous state, 33 in a compound heterozygous state, and three in a heterozygous state (Greer et al. 1999; Ribeiro et al. 2001; Sun et al. 2001; Millat et al. 2001; Bauer et al. 2002; Tarugi et al. 2002; Fernandez-Valero et al. 2005; Jahnova et al. 2014; Pina-Aguilar et al. 2014; Abela et al. 2014; Imrie et al. 2015). The p.Pro1007Ala variant is described as being associated with a variant form of Niemann-Pick disease type C, which presents with a non-classical biochemical profile (Millat et al. 2001; Sun et al. 2001). Control data are unavailable for this variant, which is reported at a frequency of 0.00019 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the collective evidence the p.Pro1007Ala variant is classified as pathogenic for Niemann-Pick disease type C. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population."}], "date_last_evaluated": "2017-04-27"}], "external_ids": [{"db": "Illumina Clinical Services Laboratory", "id": "646840"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ICSL Variant Classification Criteria 09 May 2019"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/thsgk7t4/icsl_variant_classification_criteria_09_may_2019.pdf"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.4:c.3019C>G"}], "sequence_locations": [{"assembly": "GRCh37", "chr": "18", "start": 21118528, "stop": 21118528, "variant_length": 1, "reference_allele": "G", "alternate_allele": "C"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}}, {"id": 1193540, "submission_id": {"local_key": "NM_000271.4:c.3019C>G|OMIM:257220", "submitter": "Fulgent Genetics, Fulgent Genetics", "submitted_assembly": "GRCh37", "submitter_date": "2017-05-23"}, "clinvar_accession": {"acc": "SCV000611221", "version": 1, "type": "SCV", "date_updated": "2015-10-11", "date_created": "2015-10-11", "org_id": "500105", "org_type": "primary", "org_category": "clinic"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2017-05-18"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.4:c.3019C>G"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}}, {"id": 1248998, "submission_id": {"local_key": "1801180|MedGen:C3179455", "submitter": "Invitae", "submitted_assembly": "GRCh37", "submitter_date": "2023-01-10"}, "clinvar_accession": {"acc": "SCV000650843", "version": 7, "type": "SCV", "date_updated": "2023-02-07", "date_created": "2017-12-26", "org_id": "500031", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "10521290"}]}, {"ids": [{"source": "PubMed", "value": "11754101"}]}, {"ids": [{"source": "PubMed", "value": "14639697"}]}, {"ids": [{"source": "PubMed", "value": "23183285"}]}, {"ids": [{"source": "PubMed", "value": "23791518"}]}, {"ids": [{"source": "PubMed", "value": "25425405"}]}, {"ids": [{"source": "PubMed", "value": "26981555"}]}, {"ids": [{"source": "PubMed", "value": "15937921"}]}], "comments": [{"text": "This sequence change replaces proline, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 1007 of the NPC1 protein (p.Pro1007Ala). This variant is present in population databases (rs80358257, gnomAD 0.02%). This missense change has been observed in individual(s) with Niemann-Pick type C disease (PMID: 10521290, 11754101, 14639697, 23183285, 23791518, 25425405, 26981555). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2966). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt NPC1 protein function. Experimental studies have shown that this missense change does not substantially affect NPC1 function (PMID: 15937921). For these reasons, this variant has been classified as Pathogenic."}], "date_last_evaluated": "2022-10-31"}], "external_ids": [{"db": "Invitae", "id": "1801180"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Invitae Variant Classification Sherloc (09022015)"}, "citations": [{"ids": [{"source": "PubMed", "value": "28492532"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NC_000018.9:g.21118528G>C"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "MedGen", "id": "C3179455", "type": "CUI"}]}]}, "citations": [{"ids": [{"source": "PubMed", "value": "28492532"}], "type": "general"}]}, {"id": 1414916, "submission_id": {"local_key": "NM_000271.4:c.3019C>G|OMIM:257220", "submitter": "Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen", "submitted_assembly": "GRCh37", "submitter_date": "2018-04-04"}, "clinvar_accession": {"acc": "SCV000733755", "version": 1, "type": "SCV", "date_updated": "2018-04-09", "date_created": "2018-04-09", "org_id": "506382", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion criteria provided", "descriptions": ["pathogenic"]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.4:c.3019C>G"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}, "study_name": "VKGL Data-share Consensus"}, {"id": 1451196, "submission_id": {"local_key": "NM_000271.4:c.3019C>G|OMIM:257220", "submitter": "Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center", "submitted_assembly": "GRCh37", "submitter_date": "2018-04-09"}, "clinvar_accession": {"acc": "SCV000744742", "version": 1, "type": "SCV", "date_updated": "2018-04-09", "date_created": "2018-04-09", "org_id": "506497", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "flagged submission", "descriptions": ["uncertain significance"], "date_last_evaluated": "2017-08-02"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACGS Guidelines, 2013"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/zo8lkdib/evaluation_and_reporting_of_sequence_variants_bpgs_june_2013_finalpdf.pdf"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.4:c.3019C>G"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}, "study_name": "VKGL Data-share Consensus", "comments": [{"text": "Reason: This record appears to be redundant with a more recent record from the same submitter.", "type": "FlaggedComment", "datasource": "NCBI"}, {"text": "Notes: SCV000744742 appears to be redundant with SCV001970102.", "type": "FlaggedComment", "datasource": "NCBI"}]}, {"id": 1452151, "submission_id": {"local_key": "NM_000271.4:c.3019C>G|OMIM:257220", "submitter": "Genome Diagnostics Laboratory, Amsterdam University Medical Center", "submitted_assembly": "GRCh37", "submitter_date": "2018-04-09"}, "clinvar_accession": {"acc": "SCV000745697", "version": 1, "type": "SCV", "date_updated": "2018-04-09", "date_created": "2018-04-09", "org_id": "506453", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion criteria provided", "descriptions": ["likely pathogenic"], "date_last_evaluated": "2016-11-03"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACGS Guidelines, 2013"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/zo8lkdib/evaluation_and_reporting_of_sequence_variants_bpgs_june_2013_finalpdf.pdf"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.4:c.3019C>G"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}, "study_name": "VKGL Data-share Consensus"}, {"id": 2246660, "submission_id": {"local_key": "NC_000018.9:g.21118528G>C|OMIM:257220", "submitter": "Mendelics", "submitted_assembly": "GRCh37", "submitter_date": "2019-10-22"}, "clinvar_accession": {"acc": "SCV001140857", "version": 1, "type": "SCV", "date_updated": "2020-01-09", "date_created": "2020-01-09", "org_id": "500035", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2019-05-28"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Mendelics Assertion Criteria 2017"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/chhjzatu/mendelics_assertion_criteria_2017.pdf"}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NC_000018.9:g.21118528G>C"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}}, {"id": 2354451, "submission_id": {"local_key": "15168|OMIM:257220", "submitter": "Myriad Genetics, Inc.", "submitted_assembly": "GRCh37", "submitter_date": "2020-06-18"}, "clinvar_accession": {"acc": "SCV001193996", "version": 2, "type": "SCV", "date_updated": "2020-07-03", "date_created": "2020-04-06", "org_id": "507240", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "replaced_list": [{"accession": "SCV000220180", "version": 1, "date_changed": "2020-07-01"}], "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "16098014"}]}, {"ids": [{"source": "PubMed", "value": "11479732"}]}, {"ids": [{"source": "PubMed", "value": "11333381"}]}], "comments": [{"text": "NM_000271.4(NPC1):c.3019C>G(P1007A) is classified as pathogenic in the context of Niemann-Pick disease type C1. Sources cited for classification include the following: PMID 16098014, 11479732 and 11333381. Classification of NM_000271.4(NPC1):c.3019C>G(P1007A) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.\u00e2\u20ac\u0161\u00c3\u201e\u00c3\u00b6\u00e2\u02c6\u0161\u00c3\u2018\u00e2\u02c6\u0161\u00c2\u00a3"}], "date_last_evaluated": "2019-12-24"}], "external_ids": [{"db": "Myriad Women's Health, Inc.", "id": "15168"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019)"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/vlxza0ea/myriad_women_s_health_autosomal_recessive_and_x-linked_classification_criteria_2019_.pdf"}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "sequence_locations": [{"assembly": "GRCh37", "chr": "18", "start": 21118528, "stop": 21118528, "variant_length": 1, "reference_allele": "G", "alternate_allele": "C"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}}, {"id": 2869110, "submission_id": {"local_key": "NM_000271.5:c.3019C>G|Niemann-Pick disease type C1", "submitter": "Natera, Inc.", "submitted_assembly": "GRCh37", "submitter_date": "2020-12-28"}, "clinvar_accession": {"acc": "SCV001453835", "version": 1, "type": "SCV", "date_updated": "2021-01-02", "date_created": "2021-01-02", "org_id": "500034", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion criteria provided", "descriptions": ["pathogenic"], "date_last_evaluated": "2020-09-16"}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.5:c.3019C>G"}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "Niemann-Pick disease type C1"}}]}]}}, {"id": 3003523, "submission_id": {"local_key": "NM_000271.4:c.3019C>G|OMIM:257220", "submitter": "Baylor Genetics", "submitted_assembly": "GRCh37", "submitter_date": "2021-03-05"}, "clinvar_accession": {"acc": "SCV001528308", "version": 1, "type": "SCV", "date_updated": "2021-03-22", "date_created": "2021-03-22", "org_id": "1006", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "14639697"}]}, {"ids": [{"source": "PubMed", "value": "23773996"}]}, {"ids": [{"source": "PubMed", "value": "23791518"}]}, {"ids": [{"source": "PubMed", "value": "23427322"}]}, {"ids": [{"source": "PubMed", "value": "26666848"}]}], "comments": [{"text": "This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported as disease causing for Niemann-Pick disease, type C [PMID 14639697, 23773996, 23791518, 23427322, 26666848]"}], "date_last_evaluated": "2018-10-28"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "paternal", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.4:c.3019C>G"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}}, {"id": 3061314, "submission_id": {"local_key": "a3ec321b55d34fedb36483f21da2792e", "submitter": "Centre for Inherited Metabolic Diseases, Karolinska University Hospital", "submitted_assembly": "GRCh37", "submitter_date": "2021-04-07"}, "clinvar_accession": {"acc": "SCV001554476", "version": 1, "type": "SCV", "date_updated": "2021-04-13", "date_created": "2021-04-13", "org_id": "319999", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2021-04-07"}], "external_ids": [{"db": "Centre for Inherited Metabolic Diseases", "id": "a3ec321b55d34fedb36483f21da2792e"}], "attributes": [{"attribute": {"type": "ModeOfInheritance", "value": "Autosomal recessive inheritance"}}, {"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "number_tested": 1, "family_data": {"family_history": "no"}, "proband": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "NumberMosaic", "integer_value": 0}}, {"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "SecondaryFinding", "value": "no"}}, {"attribute": {"type": "SampleLocalID", "value": "20210407-16"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.5:c.3019C>G"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}], "xrefs": [{"db": "dbSNP", "id": "80358257", "type": "rsNumber"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}}, {"id": 3965424, "submission_id": {"local_key": "18ff5194c97230fe30e5ccfe097e44107427ffb8e076b0f65340ca59a71c7f32|OMIM:257220", "submitter": "PerkinElmer Genomics", "submitted_assembly": "GRCh37", "submitter_date": "2023-03-01"}, "clinvar_accession": {"acc": "SCV002018351", "version": 2, "type": "SCV", "date_updated": "2023-03-11", "date_created": "2021-11-29", "org_id": "167595", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2020-02-27"}], "external_ids": [{"db": "PerkinElmer Genomics", "id": "18ff5194c97230fe30e5ccfe097e44107427ffb8e076b0f65340ca59a71c7f32"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.5:c.3019C>G"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}}, {"id": 4124476, "submission_id": {"local_key": "NXST941.2|MedGen:C3179455", "submitter": "DASA", "submitted_assembly": "GRCh38", "submitter_date": "2022-04-01"}, "clinvar_accession": {"acc": "SCV002107103", "version": 2, "type": "SCV", "date_updated": "2022-04-02", "date_created": "2022-03-19", "org_id": "508087", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "12955717"}]}, {"ids": [{"source": "PubMed", "value": "20554533"}]}, {"ids": [{"source": "PubMed", "value": "14639697"}]}, {"ids": [{"source": "PubMed", "value": "23773996"}]}, {"ids": [{"source": "PubMed", "value": "23791518"}]}, {"ids": [{"source": "PubMed", "value": "23427322"}]}, {"ids": [{"source": "PubMed", "value": "26666848"}]}], "comments": [{"text": "Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 12955717; 20554533) - PS3_moderate.The c.3019C>G;p.(Pro1007Ala) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 2966; PMID 14639697; PMID: 23773996; PMID: 23791518; PMID: 23427322; PMID: 26666848) - PS4. The variant is located in a mutational hot spot and/or critical and well-established functional domain PM1. The variant is present at low allele frequencies population databases (rs80358257 \u2013 gnomAD 0.001167%; ABraOM 0.000427 frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Pro1007Ala) was detected in trans with a pathogenic variant (PMID 14639697; PMID: 23773996; PMID: 23791518) - PM3. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is pathogenic."}], "date_last_evaluated": "2022-03-05"}], "external_ids": [{"db": "GeneOne, DASA", "id": "NXST941.2"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "germline", "geographic_origin": "Brazil", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "gender": "female"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "Location", "value": "NM_000271.5:exon 20"}, {"type": "HGVS", "value": "NM_000271.5:c.3019C>G"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}], "xrefs": [{"db": "dbSNP", "id": "80358257", "type": "rsNumber"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "MedGen", "id": "C3179455", "type": "CUI"}]}]}}, {"id": 7113821, "submission_id": {"local_key": "4275d57a3795301e451ef06f3273d359", "submitter": "Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein", "submitted_assembly": "GRCh38", "submitter_date": "2023-03-01"}, "clinvar_accession": {"acc": "SCV003807753", "version": 1, "type": "SCV", "date_updated": "2023-03-04", "date_created": "2023-03-04", "org_id": "508506", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "comments": [{"text": "ACMG classification criteria: PS4 strong, PM2 supporting, PM3 very strong, PP1 supporting, PP3 supporting"}], "date_last_evaluated": "2022-09-09"}], "external_ids": [{"db": "Laboratorio de Genetica e Diagnostico Molecular", "id": "cac216b151cbe5a3d184b5f99dee1da9"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "germline", "geographic_origin": "Brazil", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "number_tested": 1}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}], "traits": {"type": "Finding", "traits": [{"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002033"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001511"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0008883"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0007325"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001332"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001518"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001622"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001263"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001531"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0012736"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001508"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001562"}]}]}}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.5:c.3019C>G"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}}, {"id": 7535856, "submission_id": {"local_key": "4093815_NM_000271.5:c.3019C>G|OMIM:257220", "submitter": "Institute of Human Genetics, University of Leipzig Medical Center", "submitted_assembly": "GRCh37", "submitter_date": "2023-08-16"}, "clinvar_accession": {"acc": "SCV004027757", "version": 1, "type": "SCV", "date_updated": "2023-08-26", "date_created": "2023-08-26", "org_id": "506086", "org_type": "primary", "org_category": "clinic"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "comments": [{"text": "Identified as compund heterozygous with NM_000271.5:c.1997G>A. Criteria applied: PM3_VSTR,PM5,PM2_SUP,PP3"}], "date_last_evaluated": "2023-07-24"}], "external_ids": [{"db": "Institute of Human Genetics", "id": "4093815_NM_000271.5:c.3019C>G"}], "attributes": [{"attribute": {"type": "ModeOfInheritance", "value": "Autosomal recessive inheritance"}}, {"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "maternal", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "gender": "female"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}], "traits": {"type": "Finding", "traits": [{"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001744"}]}]}}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000271.5:c.3019C>G"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "NPC1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "257220", "type": "MIM"}]}]}}]} -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000004477", "version": 31, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2013-04-04"}, "record_status": "current", "clinical_significance": {"review_status": "criteria provided, multiple submitters, no conflicts", "description": "pathogenic", "date_last_evaluated": "2022-11-11"}, "assertion": "variation to disease", "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "number_tested": 1}, "methods": ["clinical testing", "clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}]}, {"sample": {"origin": "germline", "ethnicity": "AMR", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["research"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}]}, {"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "not provided"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "See 606530.0001 and Cali et al. (1991)."}, "citations": [{"ids": [{"source": "PubMed", "value": "2019602"}], "type": "general"}]}]}, {"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing", "literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}]}, {"sample": {"origin": "inherited", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "NumberMosaic", "integer_value": 0}}, {"attribute": {"type": "SecondaryFinding", "value": "no"}}]}, {"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "acc": "VCV000004255", "version": 38, "measures": [{"type": "single nucleotide variant", "names": [{"value": {"type": "Preferred", "value": "NM_000784.4(CYP27A1):c.1183C>T (p.Arg395Cys)"}}, {"value": {"type": "Alternate", "value": "R362C"}, "xrefs": [{"db": "OMIM", "id": "606530.0002", "type": "Allelic variant"}]}], "canonical_spdi": "NC_000002.12:218814185:C:T", "attributes": [{"type": "HGVS, coding, RefSeq", "value": "NM_000784.4:c.1183C>T"}, {"type": "HGVS, genomic, RefSeqGene", "value": "NG_007959.1:g.37438C>T"}, {"type": "HGVS, genomic, top level", "value": "NC_000002.12:g.218814186C>T", "integer_value": 38}, {"type": "HGVS, genomic, top level, previous", "value": "NC_000002.11:g.219678909C>T", "integer_value": 37}, {"type": "HGVS, previous", "value": "NM_000784.3:c.1183C>T"}, {"type": "HGVS, protein", "value": "Q02318:p.Arg395Cys"}, {"type": "HGVS, protein, RefSeq", "value": "NP_000775.1:p.Arg395Cys"}, {"type": "Location", "value": "NM_000784.3:exon 6"}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_000784.4:c.1183C>T"}]}, {"type": "nucleotide change", "value": "c.1183C>T"}, {"type": "ProteinChange1LetterCode", "value": "R395C"}, {"type": "ProteinChange3LetterCode", "value": "ARG362CYS"}], "cytogenic_locations": ["2q35"], "sequence_locations": [{"assembly": "GRCh38", "chr": "2", "accession": "NC_000002.12", "start": 218814186, "stop": 218814186, "display_start": 218814186, "display_stop": 218814186, "variant_length": 1, "assembly_accession_version": "GCF_000001405.38", "assembly_status": "current", "position_vcf": 218814186, "reference_allele_vcf": "C", "alternate_allele_vcf": "T"}, {"assembly": "GRCh37", "chr": "2", "accession": "NC_000002.11", "start": 219678909, "stop": 219678909, "display_start": 219678909, "display_stop": 219678909, "variant_length": 1, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous", "position_vcf": 219678909, "reference_allele_vcf": "C", "alternate_allele_vcf": "T"}], "measure_relationship": [{"type": "within single gene", "names": [{"value": {"type": "Preferred", "value": "cytochrome P450 family 27 subfamily A member 1"}}], "symbols": [{"value": {"type": "Preferred", "value": "CYP27A1"}}], "sequence_locations": [{"assembly": "GRCh38", "chr": "2", "accession": "NC_000002.12", "start": 218782147, "stop": 218815293, "display_start": 218782147, "display_stop": 218815293, "strand": "+", "assembly_accession_version": "GCF_000001405.38", "assembly_status": "current"}, {"assembly": "GRCh37", "chr": "2", "accession": "NC_000002.11", "start": 219646471, "stop": 219680015, "display_start": 219646471, "display_stop": 219680015, "strand": "+", "variant_length": 33545, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous"}], "xrefs": [{"db": "Gene", "id": "1593"}, {"db": "OMIM", "id": "606530", "type": "MIM"}, {"db": "HGNC", "id": "HGNC:2605"}]}], "xrefs": [{"db": "Illumina Laboratory Services, Illumina", "id": "788326"}, {"db": "UniProtKB", "id": "Q02318#VAR_001303"}, {"db": "OMIM", "id": "606530.0002", "type": "Allelic variant"}, {"db": "dbSNP", "id": "121908096", "type": "rs"}], "id": 19294}], "names": [{"value": {"type": "Preferred", "value": "NM_000784.4(CYP27A1):c.1183C>T (p.Arg395Cys)"}}, {"value": {"type": "Preferred", "value": "NM_000784.4(CYP27A1):c.1183C>T (p.Arg395Cys)"}}, {"value": {"type": "Preferred", "value": "NM_000784.4(CYP27A1):c.1183C>T (p.Arg395Cys)"}}], "attributes": [{"type": "SubmitterVariantId", "value": "GDX:674879"}, {"type": "SubmitterVariantId", "value": "ALLELE_2953"}], "xrefs": [{"db": "ClinGen", "id": "CA340211"}], "id": 4255}, "traits": {"type": "Disease", "traits": [{"type": "Disease", "names": [{"value": {"type": "Preferred", "value": "Cholestanol storage disease"}, "xrefs": [{"db": "SNOMED CT", "id": "63246000"}]}, {"value": {"type": "Alternate", "value": "Cerebral cholesterinosis"}}, {"value": {"type": "Alternate", "value": "CTX: Cerebrotendinous xanthomatosis"}}, {"value": {"type": "Alternate", "value": "Cerebrotendinous Xanthomatosis"}, "xrefs": [{"db": "GeneReviews", "id": "NBK1409"}]}], "symbols": [{"value": {"type": "Preferred", "value": "CTX"}, "xrefs": [{"db": "OMIM", "id": "213700", "type": "MIM"}]}], "attributes": [{"value": {"type": "public definition", "value": "Cerebrotendinous xanthomatosis (CTX) is a lipid storage disease characterized by infantile-onset diarrhea, childhood-onset cataract, adolescent- to young adult-onset tendon xanthomas, and adult-onset progressive neurologic dysfunction (dementia, psychiatric disturbances, pyramidal and/or cerebellar signs, dystonia, atypical parkinsonism, peripheral neuropathy, and seizures). Chronic diarrhea from infancy and/or neonatal cholestasis may be the earliest clinical manifestation. In approximately 75% of affected individuals, cataracts are the first finding, often appearing in the first decade of life. Xanthomas appear in the second or third decade; they occur on the Achilles tendon, the extensor tendons of the elbow and hand, the patellar tendon, and the neck tendons. Xanthomas have been reported in the lung, bones, and central nervous system. Some individuals show cognitive impairment from early infancy, whereas the majority have normal or only slightly impaired intellectual function until puberty; dementia with slow deterioration in intellectual abilities occurs in the third decade in more than 50% of individuals. Neuropsychiatric symptoms such as behavioral changes, hallucinations, agitation, aggression, depression, and suicide attempts may be prominent. Pyramidal signs (i.e., spasticity) and/or cerebellar signs almost invariably become evident between ages 20 and 30 years. The biochemical abnormalities that distinguish CTX from other conditions with xanthomas include high plasma and tissue cholestanol concentration, normal-to-low plasma cholesterol concentration, decreased chenodeoxycholic acid (CDCA), increased concentration of bile alcohols and their glyconjugates, and increased concentrations of cholestanol and apolipoprotein B in cerebrospinal fluid."}, "xrefs": [{"db": "GeneReviews", "id": "NBK1409"}]}, {"value": {"type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "5622"}]}], "citations": [{"ids": [{"source": "PubMed", "value": "20301583"}, {"source": "BookShelf", "value": "NBK1409"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "MONDO", "id": "MONDO:0008948"}, {"db": "MedGen", "id": "C0238052"}, {"db": "Orphanet", "id": "909"}, {"db": "OMIM", "id": "213700", "type": "MIM"}]}], "id": 1177}, "date_created": "2013-04-04", "date_last_updated": "2023-12-09", "id": 61980}, "record_status": "current", "title": "NM_000784.4(CYP27A1):c.1183C>T (p.Arg395Cys) AND Cholestanol storage disease", "clinvar_assertions": [{"id": 24650, "submission_id": {"local_key": "606530.0002_CEREBROTENDINOUS XANTHOMATOSIS", "submitter": "OMIM", "title": "CYP27A1, ARG362CYS_CEREBROTENDINOUS XANTHOMATOSIS", "submitter_date": "2010-04-08"}, "clinvar_accession": {"acc": "SCV000024650", "version": 1, "type": "SCV", "date_updated": "2013-04-04", "date_created": "2013-04-04", "org_id": "3", "org_type": "primary", "org_category": "resource"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion criteria provided", "descriptions": ["pathogenic"], "date_last_evaluated": "1991-04-25"}], "external_ids": [{"db": "OMIM", "id": "606530.0002", "type": "Allelic variant"}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human"}, "affected_status": "not provided"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "See 606530.0001 and Cali et al. (1991)."}, "citations": [{"ids": [{"source": "PubMed", "value": "2019602"}]}]}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "names": [{"value": {"type": "Preferred", "value": "CYP27A1, ARG362CYS"}}], "attributes": [{"type": "NonHGVS", "value": "ARG362CYS"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CYP27A1"}}]}], "xrefs": [{"db": "OMIM", "id": "606530.0002", "type": "Allelic variant"}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "CEREBROTENDINOUS XANTHOMATOSIS"}}]}]}}, {"id": 145873, "submission_id": {"local_key": "NM_000784.4:c.1183C>T|OMIM:213700", "submitter": "GeneReviews", "submitted_assembly": "not applicable", "submitter_date": "2022-03-29"}, "clinvar_accession": {"acc": "SCV000087137", "version": 3, "type": "SCV", "date_updated": "2022-10-01", "date_created": "2013-10-01", "org_id": "500062", "org_type": "primary", "org_category": "resource"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion provided", "descriptions": ["not provided"], "citations": [{"ids": [{"source": "PubMed", "value": "19092443"}]}, {"ids": [{"source": "BookShelf", "value": "NBK1409"}]}], "comments": [{"text": "Founder variant in Israeli Druze [Falik-Zaccai et al 2008]"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000784.4:c.1183C>T"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "MedGen", "id": "C0238052", "type": "CUI"}]}]}}, {"id": 740997, "submission_id": {"local_key": "798566", "submitter": "Illumina Laboratory Services, Illumina", "submitted_assembly": "GRCh37", "submitter_date": "2019-02-01"}, "clinvar_accession": {"acc": "SCV000427476", "version": 3, "type": "SCV", "date_updated": "2019-05-27", "date_created": "2016-12-06", "org_id": "504895", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "25983621"}]}, {"ids": [{"source": "PubMed", "value": "2019602"}]}, {"ids": [{"source": "PubMed", "value": "17697869"}]}, {"ids": [{"source": "PubMed", "value": "18227423"}]}, {"ids": [{"source": "PubMed", "value": "21645175"}]}, {"ids": [{"source": "PubMed", "value": "10775536"}]}, {"ids": [{"source": "PubMed", "value": "24746394"}]}, {"ids": [{"source": "PubMed", "value": "26156051"}]}, {"ids": [{"source": "PubMed", "value": "26906304"}]}], "comments": [{"text": "Across a selection of the available literature, the CYP27A1 c.1183C>T (p.Arg395Cys) variant has been reported in nine studies in which is found in a total of 20 individuals with cerebrotendinous xanthomatosis, including four in a homozygous state and 16 in a compound heterozygous state, and in at least 18 additional disease alleles of unknown zygosity (Cali et al. 1991; Verrips et al. 2000; Szlago et al. 2008; Pilo-de-la-Fuente et al. 2011; Lionnet et al. 2014; Smally et al. 2015; Varman et al. 2016; Huidekoper et al. 2016; Koopal et al. 2016). The p.Arg395Cys variant was absent from 310 control alleles but is reported at a frequency of 0.00021 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies by Cali et al. (1991) showed the p.Arg395Cys variant had no detectable sterol 27-hydroxylase enzyme activity when expressed in COS-M6 cells. Gupta et al. (2007) demonstrated in COS-1 cells that the variant resulted in lower levels of protein expression and disrupted the heme-binding domain, resulting in an inactive protein. Based on the collective evidence, the p.Arg395Cys variant is classified pathogenic for cerebrotendinous xanthomatosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population."}], "date_last_evaluated": "2017-04-28"}], "external_ids": [{"db": "Illumina Clinical Services Laboratory", "id": "788326"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ICSL Variant Classification Criteria 09 May 2019"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/thsgk7t4/icsl_variant_classification_criteria_09_may_2019.pdf"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000784.3:c.1183C>T"}], "sequence_locations": [{"assembly": "GRCh37", "chr": "2", "start": 219678909, "stop": 219678909, "variant_length": 1, "reference_allele": "C", "alternate_allele": "T"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CYP27A1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "213700", "type": "MIM"}]}]}}, {"id": 1450627, "submission_id": {"local_key": "NM_000784.3:c.1183C>T|OMIM:213700", "submitter": "Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center", "submitted_assembly": "GRCh37", "submitter_date": "2018-04-09"}, "clinvar_accession": {"acc": "SCV000744173", "version": 1, "type": "SCV", "date_updated": "2016-12-06", "date_created": "2016-12-06", "org_id": "506497", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "flagged submission", "descriptions": ["likely pathogenic"], "date_last_evaluated": "2017-12-08"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACGS Guidelines, 2013"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/zo8lkdib/evaluation_and_reporting_of_sequence_variants_bpgs_june_2013_finalpdf.pdf"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000784.3:c.1183C>T"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CYP27A1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "213700", "type": "MIM"}]}]}, "study_name": "VKGL Data-share Consensus", "comments": [{"text": "Reason: This record appears to be redundant with a more recent record from the same submitter.", "type": "FlaggedComment", "datasource": "NCBI"}, {"text": "Notes: SCV000744173 appears to be redundant with SCV001965692.", "type": "FlaggedComment", "datasource": "NCBI"}]}, {"id": 1464433, "submission_id": {"local_key": "2780495|MedGen:C0238052", "submitter": "Invitae", "submitted_assembly": "GRCh37", "submitter_date": "2023-01-10"}, "clinvar_accession": {"acc": "SCV000754983", "version": 7, "type": "SCV", "date_updated": "2023-02-07", "date_created": "2018-05-03", "org_id": "500031", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "2019602"}]}, {"ids": [{"source": "PubMed", "value": "10775536"}]}, {"ids": [{"source": "PubMed", "value": "18227423"}]}, {"ids": [{"source": "PubMed", "value": "20402754"}]}, {"ids": [{"source": "PubMed", "value": "21645175"}]}, {"ids": [{"source": "PubMed", "value": "21955034"}]}, {"ids": [{"source": "PubMed", "value": "24746394"}]}, {"ids": [{"source": "PubMed", "value": "26156051"}]}, {"ids": [{"source": "PubMed", "value": "26906304"}]}, {"ids": [{"source": "PubMed", "value": "2019602"}]}, {"ids": [{"source": "PubMed", "value": "8950197"}]}, {"ids": [{"source": "PubMed", "value": "9790667"}]}], "comments": [{"text": "This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 395 of the CYP27A1 protein (p.Arg395Cys). This variant is present in population databases (rs121908096, gnomAD 0.05%). This missense change has been observed in individuals with cerebrotendinous xanthomatosis (PMID: 2019602, 10775536, 18227423, 20402754, 21645175, 21955034, 24746394, 26156051, 26906304). This variant is also known as p.Arg362Cys. ClinVar contains an entry for this variant (Variation ID: 4255). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: \"Deleterious\"; PolyPhen-2: \"Probably Damaging\"; Align-GVGD: \"Class C0\"). Experimental studies have shown that this missense change affects CYP27A1 function (PMID: 2019602). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant disrupts the p.Arg395 amino acid residue in CYP27A1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8950197, 9790667). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic."}], "date_last_evaluated": "2022-11-01"}], "external_ids": [{"db": "Invitae", "id": "2780495"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Invitae Variant Classification Sherloc (09022015)"}, "citations": [{"ids": [{"source": "PubMed", "value": "28492532"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NC_000002.11:g.219678909C>T"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CYP27A1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "MedGen", "id": "C0238052", "type": "CUI"}]}]}, "citations": [{"ids": [{"source": "PubMed", "value": "28492532"}], "type": "general"}]}, {"id": 1764352, "submission_id": {"local_key": "SUB5479855", "submitter": "Unidad de Gen\u00f3mica M\u00e9dica UC, Pontificia Universidad Cat\u00f3lica de Chile", "title": "SUB5479855", "submitted_assembly": "GRCh38", "submitter_date": "2019-04-30"}, "clinvar_accession": {"acc": "SCV000897998", "version": 1, "type": "SCV", "date_updated": "2019-05-02", "date_created": "2019-05-02", "org_id": "506969", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "comments": [{"text": "This patient is a compound heterozygote for the substitution c.256-1G>T that causes exon 2 skipping, leading to a premature stop codon in exon 3, and for the pathogenic mutation c.1183C>T(p.Arg395Cys).", "type": "public"}], "date_last_evaluated": "2014-04-07"}], "attributes": [{"attribute": {"type": "ModeOfInheritance", "value": "Autosomal recessive inheritance"}}, {"attribute": {"type": "AssertionMethod", "value": "Smalley et al. (Genet Mol Biol. 2015)"}, "citations": [{"ids": [{"source": "PubMed", "value": "25983621"}], "type": "general"}]}], "observed_in": [{"sample": {"origin": "germline", "ethnicity": "AMR", "geographic_origin": "Chile", "species": {"value": "human", "taxonomy_id": 9606}, "age": [{"age_unit": "years", "value": 40, "type": "minimum"}, {"age_unit": "years", "value": 49, "type": "maximum"}], "affected_status": "yes", "gender": "female"}, "methods": ["research"], "observed_data": [{"attribute": {"type": "CompoundHeterozygote", "integer_value": 1}}], "traits": {"type": "Finding", "traits": [{"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002028"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000519"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002385"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002355"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001317"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000763"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0003124"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001285"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002015"}]}, {"type": "Finding", "names": [{"value": {"type": "Preferred", "value": "Bilateral pyramidal syndrome"}}]}, {"type": "Finding", "names": [{"value": {"type": "Preferred", "value": "Elevated levels of cholestan-3-ol"}}]}], "comments": [{"text": "No history of consanguinity. History of unexplained chronic diarrhea and bilateral cataracts diagnosed at age of 5 and operated in childhood. Since age of 28 she developed paraparesis and progressive difficulty to walk. Neurological examination in that moment showed bilateral pyramidal syndrome, cerebellar syndrome and deep sensory deficit in lower extremities. Brain magnetic resonance imaging (MRI) showed involutive signs incerebellar and bilateral frontal regions, with white matter involvement bulb and cerebellum. An electrophysiological study of the lower extremities showed signs of chronic sensory-motor polyneuropathy. Laboratory tests showed negative results for HIV, HTLV-1, and VDRL. Plasma B12 and folic acid levels were normal. Thyroid function was normal. The patient showed a normal lipid profile, except for slightly elevated high density lipoprotein cholesterol (HDL-C) (74.6 mg/dL). At age of 31, CTX was suspected, although without presenting typical tendinous xanthomas. This patient showed a concentration of 64 \u00ce\u00bcmol/L of plasma cholestanol reported from an external laboratory (normal values: 2\u00e2\u20ac\u201c12.6 \u00ce\u00bcmol/L). At the moment of recruitment for this study, the patient is prostrated, with a severe spastic tetraparesis, flexor pattern of the four limbs, severe dysphagia that required installation of a percutaneous endoscopic gastrostomy. There is no clinical data of her bone condition at the moment of diagnosis. Due to her clinical condition, it was not possible to perform a bone densitometry at the moment of the recruitment.", "type": "public"}]}}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NC_000002.12:g.218814186C>T"}, {"type": "Location", "value": "NM_000784.3: exon 6"}], "measure_relationship": [{"type": "variant in gene", "names": [{"value": {"type": "Preferred", "value": "cytochrome P450 family 27 subfamily A member 1"}}], "symbols": [{"value": {"type": "Preferred", "value": "CYP27A1"}}]}], "xrefs": [{"db": "dbSNP", "id": "rs121908096"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "213700"}]}]}, "citations": [{"ids": [{"source": "PubMed", "value": "25983621"}], "type": "general"}]}, {"id": 2354456, "submission_id": {"local_key": "136568|OMIM:213700", "submitter": "Myriad Genetics, Inc.", "submitted_assembly": "GRCh37", "submitter_date": "2020-06-18"}, "clinvar_accession": {"acc": "SCV001194001", "version": 2, "type": "SCV", "date_updated": "2020-07-03", "date_created": "2020-04-06", "org_id": "507240", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "replaced_list": [{"accession": "SCV000788833", "version": 2, "date_changed": "2020-07-02"}], "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "2019602"}]}, {"ids": [{"source": "PubMed", "value": "10775536"}]}, {"ids": [{"source": "PubMed", "value": "21955034"}]}, {"ids": [{"source": "PubMed", "value": "21645175"}]}], "comments": [{"text": "NM_000784.3(CYP27A1):c.1183C>T(R395C) is classified as pathogenic in the context of cerebrotendinous xanthomatosis. Sources cited for classification include the following: PMID 2019602, 10775536, 21955034 and 21645175. Classification of NM_000784.3(CYP27A1):c.1183C>T(R395C) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening."}], "date_last_evaluated": "2019-12-26"}], "external_ids": [{"db": "Myriad Women's Health, Inc.", "id": "136568"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019)"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/vlxza0ea/myriad_women_s_health_autosomal_recessive_and_x-linked_classification_criteria_2019_.pdf"}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "sequence_locations": [{"assembly": "GRCh37", "chr": "2", "start": 219678909, "stop": 219678909, "variant_length": 1, "reference_allele": "C", "alternate_allele": "T"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CYP27A1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "213700", "type": "MIM"}]}]}}, {"id": 2871061, "submission_id": {"local_key": "NM_000784.4:c.1183C>T|Cerebrotendinous xanthomatosis", "submitter": "Natera, Inc.", "submitted_assembly": "GRCh37", "submitter_date": "2020-12-28"}, "clinvar_accession": {"acc": "SCV001455786", "version": 1, "type": "SCV", "date_updated": "2021-01-02", "date_created": "2021-01-02", "org_id": "500034", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion criteria provided", "descriptions": ["pathogenic"], "date_last_evaluated": "2020-09-16"}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000784.4:c.1183C>T"}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "Cerebrotendinous xanthomatosis"}}]}]}}, {"id": 2996053, "submission_id": {"local_key": "34429|OMIM:213700", "submitter": "Baylor Genetics", "submitted_assembly": "GRCh37", "submitter_date": "2023-02-19"}, "clinvar_accession": {"acc": "SCV001520838", "version": 2, "type": "SCV", "date_updated": "2023-03-11", "date_created": "2021-03-22", "org_id": "1006", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2022-11-11"}], "external_ids": [{"db": "Baylor Genetics", "id": "34429"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000784.4:c.1183C>T"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "213700", "type": "MIM"}]}]}}, {"id": 3966897, "submission_id": {"local_key": "4e0fe755bdf5c496b9467f123b2abe03f7855de5e2f85161b1930cd97227068f|OMIM:213700", "submitter": "PerkinElmer Genomics", "submitted_assembly": "GRCh37", "submitter_date": "2023-03-01"}, "clinvar_accession": {"acc": "SCV002018129", "version": 2, "type": "SCV", "date_updated": "2023-03-11", "date_created": "2021-11-29", "org_id": "167595", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2021-03-12"}], "external_ids": [{"db": "PerkinElmer Genomics", "id": "4e0fe755bdf5c496b9467f123b2abe03f7855de5e2f85161b1930cd97227068f"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000784.4:c.1183C>T"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "213700", "type": "MIM"}]}]}}, {"id": 4902747, "submission_id": {"local_key": "NM_000784.4:c.1183C>T", "submitter": "New York Genome Center", "submitted_assembly": "GRCh38", "submitter_date": "2022-05-05"}, "clinvar_accession": {"acc": "SCV002506658", "version": 1, "type": "SCV", "date_updated": "2022-05-16", "date_created": "2022-05-16", "org_id": "507558", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2021-04-30"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "NYGC Assertion Criteria 2020"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/hhfhf6ms/nygc_assertion_criteria_2020.pdf"}]}], "observed_in": [{"sample": {"origin": "inherited", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "NumberMosaic", "integer_value": 0}}, {"attribute": {"type": "SingleHeterozygote", "integer_value": 1}}, {"attribute": {"type": "SecondaryFinding", "value": "no"}}], "traits": {"type": "Finding", "traits": [{"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001250"}]}]}}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000784.4:c.1183C>T"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "213700", "type": "MIM"}]}]}, "study_name": "CSER-NYCKidSeq"}, {"id": 5414599, "submission_id": {"local_key": "vcgs/unit_1/hg38_NM_000784_3_CYP27A1_c_1183C_T", "submitter": "Victorian Clinical Genetics Services, Murdoch Childrens Research Institute", "submitter_date": "2022-12-21"}, "clinvar_accession": {"acc": "SCV002769446", "version": 1, "type": "SCV", "date_updated": "2022-12-24", "date_created": "2022-12-24", "org_id": "500104", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "additional_submitters": [{"type": "behalf", "submitter_name": "Shariant Australia, Australian Genomics", "org_id": 508197}], "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "2019602"}]}, {"ids": [{"source": "PubMed", "value": "21645175"}]}, {"ids": [{"source": "PubMed", "value": "25983621"}]}, {"ids": [{"source": "PubMed", "value": "28324197"}]}], "comments": [{"text": "Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with cerebrotendinous xanthomatosis (MIM#213700). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine. This variant is also in a splice region (second last coding base of exon 6), however cDNA studies have shown it does not affect splicing (PMID: 25983621). (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD v2 <0.01 for a recessive condition (80 heterozygotes, 0 homozygotes). (SP) 0309 - Multiple alternative amino acid changes at the same position have been observed in gnomAD (v3) (highest allele count: 14 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated Cytochrome P450 domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has previously been reported as pathogenic, in either a homozygous or compound heterozygous state, in multiple patients with cerebrotendinous xanthomatosis (ClinVar, PMIDs: 2019602, 21645175, 28324197). (SP) 0901 - This variant has strong evidence for segregation with disease. This variant has been shown to segregate with disease in multiple families (PMIDs: 21645175, 28324197). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Transfected cells displayed reduced enzyme activity (PMID: 2019602). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign"}], "date_last_evaluated": "2022-02-02"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}, {"attribute": {"type": "ModeOfInheritance", "value": "Autosomal recessive inheritance"}}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000784.3:c.1183C>T"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CYP27A1"}}]}]}], "attributes": [{"type": "SubmitterVariantId", "value": "ALLELE_2953"}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "213700", "type": "MIM"}]}]}}, {"id": 7114310, "submission_id": {"local_key": "959ebd1a6f8da95f65381c8595f9bf8a", "submitter": "Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein", "submitted_assembly": "GRCh38", "submitter_date": "2023-03-01"}, "clinvar_accession": {"acc": "SCV003806874", "version": 1, "type": "SCV", "date_updated": "2023-03-04", "date_created": "2023-03-04", "org_id": "508506", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "comments": [{"text": "ACMG classification criteria: PS3 supporting, PS4 strong, PM3 strong, PP3 supporting"}], "date_last_evaluated": "2022-07-12"}], "external_ids": [{"db": "Laboratorio de Genetica e Diagnostico Molecular", "id": "1ade8a0e17d2f6d8618565ce7a843a9e"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "germline", "geographic_origin": "Brazil", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "number_tested": 1}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}], "traits": {"type": "Finding", "traits": [{"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001260"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002066"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001251"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001347"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000639"}]}]}}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000784.4:c.1183C>T"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CYP27A1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "213700", "type": "MIM"}]}]}}]} -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000005387", "version": 28, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2013-04-04"}, "record_status": "current", "clinical_significance": {"review_status": "criteria provided, multiple submitters, no conflicts", "description": "other", "date_last_evaluated": "2023-08-23"}, "assertion": "variation to disease", "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "number_tested": 1}, "methods": ["clinical testing", "literature only", "clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 2}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}]}, {"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "not provided"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "In 3 families, Delettre et al. (2000) found that members with autosomal dominant optic atrophy (165500) had a 4-bp deletion in exon 27 of the OPA1 gene, 2708delTTAG, that caused 2 amino acid substitutions (val903 to gly, arg904 to asp) and a premature stop at codon 905. This mutation was present in an asymptomatic carrier in one family but was fully penetrant in the other 2 families. This penetrance was expected since minimally affected patients and asymptomatic carriers (with no detectable optic atrophy on fundus examination) had been described. The 3 families were apparently unrelated, but all originated from the northern French provinces and Belgium. Founder effect had been demonstrated by haplotype studies in the British Isles (Votruba et al., 1998; Johnston et al., 1999)."}, "citations": [{"ids": [{"source": "PubMed", "value": "11017079"}], "type": "general"}, {"ids": [{"source": "PubMed", "value": "9490303"}], "type": "general"}, {"ids": [{"source": "PubMed", "value": "9917792"}], "type": "general"}]}, {"attribute": {"type": "Description", "value": "Toomes et al. (2001) haplotyped 8 unrelated individuals with the 2708delTTAG mutation and concluded that this may be a mutation hotspot and not an ancient mutation, thus excluding a major founder effect at the OPA1 locus. A recalculation of the penetrance of this disorder within 2 of 8 families indicated figures as low as 43% and 62% associated with the 2708delTTAG mutation."}, "citations": [{"ids": [{"source": "PubMed", "value": "11440989"}], "type": "general"}]}, {"attribute": {"type": "Description", "value": "In 2 sibs with clinical features of Behr syndrome (BEHRS; 210000), Schaaf et al. (2011) identified compound heterozygosity for 2 mutations in the OPA1 gene: 2708delTTAG and I382M (605290.0018). Each parent was heterozygous for 1 of the mutations. The father, who carried the truncating mutation, had mild optic atrophy and bilateral sensorineural hearing loss, whereas the mother, who carried the missense mutation, had myopia, with no evidence of optic atrophy, and mild sensorineural hearing loss. Schaaf et al. (2011) considered the more severe phenotype in the children to be consistent with semidominant inheritance."}, "citations": [{"ids": [{"source": "PubMed", "value": "21636302"}], "type": "general"}]}, {"attribute": {"type": "Description", "value": "In an 11-year-old girl with Behr syndrome, Bonneau et al. (2014) identified compound heterozygous mutations in the OPA1 gene: a 4-bp deletion (c.2708_2711) in exon 27, resulting in a frameshift and premature termination (Val903GlyfsTer), and a c.1204G-A transition in exon 12, resulting in a val402-to-met (V402M; 605290.0021) substitution."}, "citations": [{"ids": [{"source": "PubMed", "value": "25012220"}], "type": "general"}]}]}, {"sample": {"origin": "maternal", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "VariantChromosomes", "integer_value": 2}}]}, {"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "number_tested": 2}, "methods": ["clinical testing", "research", "clinical testing", "other", "other"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 2}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "SampleLocalID", "value": "genomeconnect_20489_622"}}, {"attribute": {"type": "SampleLocalID", "value": "genomeconnect_15054"}}, {"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "acc": "VCV000005082", "version": 45, "measures": [{"type": "deletion", "names": [{"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}], "canonical_spdi": "NC_000003.12:193667167:AGTTAG:AG", "attributes": [{"type": "HGVS, coding", "value": "NM_130837.3:c.2873-2_2874del"}, {"type": "HGVS, coding", "value": "NM_130837.2:c.2873_2876del"}, {"type": "HGVS, coding, LRG", "value": "LRG_337t1:c.2708_2711del"}, {"type": "HGVS, coding, LRG", "value": "LRG_337t2:c.2873_2876del"}, {"type": "HGVS, coding, RefSeq", "value": "NM_130837.3:c.2873_2876del"}, {"type": "HGVS, genomic, LRG", "value": "LRG_337:g.79027_79030del"}, {"type": "HGVS, genomic, RefSeqGene", "value": "NG_011605.1:g.79027_79030del"}, {"type": "HGVS, genomic, top level", "value": "NC_000003.12:g.193667170_193667173del", "integer_value": 38}, {"type": "HGVS, genomic, top level, other", "value": "NC_000003.11:g.193384957_193384960del", "integer_value": 37}, {"type": "HGVS, genomic, top level, previous", "value": "NC_000003.11:g.193384959_193384962del", "integer_value": 37}, {"type": "HGVS, previous", "value": "NM_015560.2:c.2708_2711delTTAG"}, {"type": "HGVS, previous", "value": "NM_130837.2:c.2873_2876delTTAG"}, {"type": "HGVS, protein"}, {"type": "HGVS, protein"}, {"type": "HGVS, protein"}, {"type": "HGVS, protein", "value": "p.(Val903Glyfs*3)"}, {"type": "HGVS, protein", "value": "p.V903GfsX3"}, {"type": "HGVS, protein", "value": "NP_056375.2:p.Val903GlyfsTer3"}, {"type": "Location", "value": "NM_015560.2:exon 27", "xrefs": [{"db": "HGMD", "id": "CD002708"}]}, {"type": "MolecularConsequence", "value": "splice acceptor variant", "xrefs": 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{"db": "OMIM", "id": "605290.0003", "type": "Allelic variant"}, {"db": "dbSNP", "id": "80356530", "type": "rs"}], "id": 20121}], "names": [{"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}, {"value": {"type": "Preferred", "value": "NM_130837.3(OPA1):c.2873_2876del"}}], "attributes": [{"type": "SubmitterVariantId", "value": "GDX:45948"}], "xrefs": [{"db": "ClinGen", "id": "CA143822"}], "id": 5082}, "traits": {"type": "Disease", "traits": [{"type": "Disease", "names": [{"value": {"type": "Preferred", "value": "Autosomal dominant optic atrophy classic form"}, "xrefs": [{"db": "SNOMED CT", "id": "717336005"}]}, {"value": {"type": "Alternate", "value": "Optic atrophy, juvenile"}}, {"value": {"type": "Alternate", "value": "Kjer-type optic atrophy"}}, {"value": {"type": "Alternate", "value": "Optic Atrophy Type 1"}, "xrefs": [{"db": "GeneReviews", "id": "NBK1248"}, {"db": "Genetic Alliance", "id": "Optic+atrophy+1/5380"}]}], "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}, "xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}, {"value": {"type": "Alternate", "value": "OAK"}, "xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}], "attributes": [{"value": {"type": "public definition", "value": "Optic atrophy type 1 (OPA1, or Kjer type optic atrophy) is characterized by bilateral and symmetric optic nerve pallor associated with insidious decrease in visual acuity (usually between ages 4 and 6 years), visual field defects, and color vision defects. Visual impairment is usually moderate (6/10 to 2/10), but ranges from mild or even insignificant to severe (legal blindness with acuity <1/20). The visual field defect is typically centrocecal, central, or paracentral; it is often large in those with severe disease. The color vision defect is often described as acquired blue-yellow loss (tritanopia). Other findings can include auditory neuropathy resulting in sensorineural hearing loss that ranges from severe and congenital to subclinical (i.e., identified by specific audiologic testing only). Visual evoked potentials are typically absent or delayed; pattern electroretinogram shows an abnormal N95:P50 ratio. Tritanopia is the classic feature of color vision defect, but more diffuse nonspecific dyschromatopsia is not uncommon. Ophthalmoscopic examination discloses temporal or diffuse pallor of the optic discs, sometimes associated with optic disc excavation. The neuroretinal rim shows some pallor in most cases, sometimes associated with a temporal pigmentary gray crescent."}, "xrefs": [{"db": "GeneReviews", "id": "NBK1248"}]}, {"value": {"type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "9890"}]}], "citations": [{"ids": [{"source": "PubMed", "value": "20301426"}, {"source": "BookShelf", "value": "NBK1248"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "MONDO", "id": "MONDO:0008134"}, {"db": "MedGen", "id": "C0338508"}, {"db": "Orphanet", "id": "98673"}, {"db": "OMIM", "id": "165500", "type": "MIM"}]}], "id": 1406}, "date_created": "2013-04-04", "date_last_updated": "2023-12-09", "id": 62890}, "record_status": "current", "title": "NM_130837.3(OPA1):c.2873_2876del AND Autosomal dominant optic atrophy classic form", "clinvar_assertions": [{"id": 25567, "submission_id": {"local_key": "605290.0003_OPTIC ATROPHY 1", "submitter": "OMIM", "title": "OPA1, 4-BP DEL, 2708TTAG_OPTIC ATROPHY 1", "submitter_date": "2016-04-07"}, "clinvar_accession": {"acc": "SCV000025567", "version": 3, "type": "SCV", "date_updated": "2016-04-09", "date_created": "2013-04-04", "org_id": "3", "org_type": "primary", "org_category": "resource"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion criteria provided", "descriptions": ["pathogenic"], "date_last_evaluated": "2011-08-01"}], "external_ids": [{"db": "OMIM", "id": "605290.0003", "type": "Allelic variant"}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human"}, "affected_status": "not provided"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "In 3 families, Delettre et al. (2000) found that members with autosomal dominant optic atrophy (165500) had a 4-bp deletion in exon 27 of the OPA1 gene, 2708delTTAG, that caused 2 amino acid substitutions (val903 to gly, arg904 to asp) and a premature stop at codon 905. This mutation was present in an asymptomatic carrier in one family but was fully penetrant in the other 2 families. This penetrance was expected since minimally affected patients and asymptomatic carriers (with no detectable optic atrophy on fundus examination) had been described. The 3 families were apparently unrelated, but all originated from the northern French provinces and Belgium. Founder effect had been demonstrated by haplotype studies in the British Isles (Votruba et al., 1998; Johnston et al., 1999)."}, "citations": [{"ids": [{"source": "PubMed", "value": "11017079"}]}, {"ids": [{"source": "PubMed", "value": "9490303"}]}, {"ids": [{"source": "PubMed", "value": "9917792"}]}], "xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}, {"attribute": {"type": "Description", "value": "Toomes et al. (2001) haplotyped 8 unrelated individuals with the 2708delTTAG mutation and concluded that this may be a mutation hotspot and not an ancient mutation, thus excluding a major founder effect at the OPA1 locus. A recalculation of the penetrance of this disorder within 2 of 8 families indicated figures as low as 43% and 62% associated with the 2708delTTAG mutation."}, "citations": [{"ids": [{"source": "PubMed", "value": "11440989"}]}]}, {"attribute": {"type": "Description", "value": "In 2 sibs with clinical features of Behr syndrome (BEHRS; 210000), Schaaf et al. (2011) identified compound heterozygosity for 2 mutations in the OPA1 gene: 2708delTTAG and I382M (605290.0018). Each parent was heterozygous for 1 of the mutations. The father, who carried the truncating mutation, had mild optic atrophy and bilateral sensorineural hearing loss, whereas the mother, who carried the missense mutation, had myopia, with no evidence of optic atrophy, and mild sensorineural hearing loss. Schaaf et al. (2011) considered the more severe phenotype in the children to be consistent with semidominant inheritance."}, "citations": [{"ids": [{"source": "PubMed", "value": "21636302"}]}], "xrefs": [{"db": "OMIM", "id": "210000", "type": "MIM"}]}, {"attribute": {"type": "Description", "value": "In an 11-year-old girl with Behr syndrome, Bonneau et al. (2014) identified compound heterozygous mutations in the OPA1 gene: a 4-bp deletion (c.2708_2711) in exon 27, resulting in a frameshift and premature termination (Val903GlyfsTer), and a c.1204G-A transition in exon 12, resulting in a val402-to-met (V402M; 605290.0021) substitution."}, "citations": [{"ids": [{"source": "PubMed", "value": "25012220"}]}]}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "names": [{"value": {"type": "Preferred", "value": "OPA1, 4-BP DEL, 2708TTAG"}}], "attributes": [{"type": "NonHGVS", "value": "4-BP DEL, 2708TTAG"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}], "xrefs": [{"db": "OMIM", "id": "605290.0003", "type": "Allelic variant"}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "OPTIC ATROPHY 1"}}]}]}}, {"id": 41284, "submission_id": {"local_key": "NM_015560.2:c.2708_2711delTTAG|OMIM:165500", "submitter": "GeneReviews", "submitter_date": "2015-11-13"}, "clinvar_accession": {"acc": "SCV000041284", "version": 3, "type": "SCV", "date_updated": "2022-10-01", "date_created": "2013-04-04", "org_id": "500062", "org_type": "primary", "org_category": "resource"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion provided", "descriptions": ["not provided"], "citations": [{"ids": [{"source": "PubMed", "value": "11440989"}]}, {"ids": [{"source": "BookShelf", "value": "NBK1248"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "names": [{"value": {"type": "Alternate", "value": "NP_056375.2:p.Val903GlyfsTer3"}}], "attributes": [{"type": "HGVS", "value": "NM_015560.2:c.2708_2711delTTAG"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "MedGen", "id": "C0338508", "type": "CUI"}]}]}}, {"id": 1174109, "submission_id": {"local_key": "genomeconnect_20489_15054", "submitter": "GenomeConnect, ClinGen", "submitted_assembly": "GRCh37", "submitter_date": "2022-02-09"}, "clinvar_accession": {"acc": "SCV000606947", "version": 2, "type": "SCV", "date_updated": "2022-02-13", "date_created": "2017-10-14", "org_id": "506185", "org_type": "primary", "org_category": "other"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion provided", "descriptions": ["not provided"], "comments": [{"text": "Variant was identified in multiple participants. Variant interpreted as Pathogenic and reported, most recently, on 11-07-2019 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant."}]}], "external_ids": [{"db": "GenomeConnect", "id": "genomeconnect_20489_622_15054_622"}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "age": [{"age_unit": "years", "value": 50, "type": "minimum"}, {"age_unit": "years", "value": 59, "type": "maximum"}], "affected_status": "yes", "number_tested": 1, "gender": "female", "indication": {"traits": [{"names": [{"value": {"type": "Preferred", "value": "Diagnostic"}}]}], "type": "Indication"}}, "methods": ["other"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "SampleLocalID", "value": "genomeconnect_20489_622"}}], "traits": {"type": "Finding", "traits": [{"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000517"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000504"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000545"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000540"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000587"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000365"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000360"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002250"}]}]}}, {"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "age": [{"age_unit": "years", "value": 40, "type": "minimum"}, {"age_unit": "years", "value": 49, "type": "maximum"}], "affected_status": "yes", "number_tested": 1, "gender": "male", "indication": {"traits": [{"names": [{"value": {"type": "Preferred", "value": "Diagnostic"}}]}], "type": "Indication"}}, "methods": ["other"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "SampleLocalID", "value": "genomeconnect_15054"}}], "traits": {"type": "Finding", "traits": [{"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002686"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000496"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000504"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000545"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000587"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001290"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000739"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000716"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000722"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0007565"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0410009"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0003011"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002577"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002242"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000479"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0002579"}]}]}}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_015560.2:c.2708_2711delTTAG"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}]}}, {"id": 1359162, "submission_id": {"local_key": "19_October 2017|OMIM:165500", "submitter": "Center of Genomic medicine, Geneva, University Hospital of Geneva", "submitted_assembly": "GRCh37", "submitter_date": "2017-11-15"}, "clinvar_accession": {"acc": "SCV000693465", "version": 2, "type": "SCV", "date_updated": "2022-12-11", "date_created": "2017-10-14", "org_id": "505593", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "comments": [{"text": "This frameshift variant (deletion of four nucleotides) in the OPA1 gene was identified in a male young patient and also his mother, both diagnosed with optic atrophy 1."}], "date_last_evaluated": "2017-09-18"}], "external_ids": [{"db": "Genome Clinic of Geneva", "id": "19_October 2017"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "maternal", "species": {"value": "human", "taxonomy_id": 9606}, "age": [{"age_unit": "years", "value": 10, "type": "minimum"}, {"age_unit": "years", "value": 19, "type": "maximum"}], "affected_status": "yes", "gender": "male"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantChromosomes", "integer_value": 2}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "names": [{"value": {"type": "Alternate", "value": "p.(Val903Glyfs*3)"}}], "attributes": [{"type": "HGVS", "value": "NM_015560.2:c.2708_2711del"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}]}}, {"id": 2993454, "submission_id": {"local_key": "NM_130837.2:c.2873_2876delTTAG|OMIM:165500", "submitter": "Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris", "submitted_assembly": "GRCh37", "submitter_date": "2021-03-14"}, "clinvar_accession": {"acc": "SCV001519161", "version": 1, "type": "SCV", "date_updated": "2021-09-19", "date_created": "2021-09-19", "org_id": "507178", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2021-01-04"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["research"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_130837.2:c.2873_2876delTTAG"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}]}}, {"id": 3047510, "submission_id": {"local_key": "NM_130837.2:c.2873_2876del|OMIM:165500", "submitter": "Institute of Medical Molecular Genetics, University of Zurich", "submitted_assembly": "GRCh37", "submitter_date": "2021-03-19"}, "clinvar_accession": {"acc": "SCV001548160", "version": 1, "type": "SCV", "date_updated": "2021-03-28", "date_created": "2021-03-28", "org_id": "300471", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["likely pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "33546218"}]}], "date_last_evaluated": "2021-01-30"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_130837.2:c.2873_2876del"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}]}, "citations": [{"ids": [{"source": "PubMed", "value": "33546218"}], "type": "general"}]}, {"id": 3878410, "submission_id": {"local_key": "NM_015560.2:c.2708_2711delTTAG|OMIM:165500", "submitter": "Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital", "submitted_assembly": "GRCh37", "submitter_date": "2021-10-04"}, "clinvar_accession": {"acc": "SCV001984459", "version": 1, "type": "SCV", "date_updated": "2021-10-30", "date_created": "2021-10-30", "org_id": "507199", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "flagged submission", "descriptions": ["pathogenic"], "date_last_evaluated": "2020-10-18"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_015560.2:c.2708_2711delTTAG"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}]}, "comments": [{"text": "The p.Val903fs variant in the OPA1 gene was previously reported in the heterozygous state in several individuals with optic atrophy (PMID: 11017079 11440989) though penetrance was incomplete ranging between 43% and 62% (PMID: 11440989). In addition this variant was also identified in the heterozygous state in another patient with optic atrophy plus spastic paraplegia Duane retraction syndrome migraine with atypical aura patent foramen ovale and muscle fibre abnormalities. However this patient's father and sister were unaffected carriers of the same variants again suggesting incomplete penetrance (PMID: 21646330). A mouse model carrying this variant displayed multi-systemic poly-degenerative phenotype with a presentation associating signs of visual failure deafness encephalomyopathy peripheral neuropathy ataxia and cardiomyopathy (PMID: 23250881). The Val903fs variant was also identified in 10/282600 (0.0035% 0 homozygotes) total alleles in the Genome Aggregation Database (gnomAD). This frameshift variant is predicted to alter the protein's amino acid sequence beginning at position 903 and lead to a premature termination codon 3 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. In summary this variant meets our criteria for pathogenicity for dominant optic atrophy with reduced penetrance."}, {"text": "Reason: This record appears to be redundant with a more recent record from the same submitter.", "type": "FlaggedComment", "datasource": "NCBI"}, {"text": "Notes: SCV001984459 appears to be redundant with SCV002818199.", "type": "FlaggedComment", "datasource": "NCBI"}]}, {"id": 4538669, "submission_id": {"local_key": "3-193384956-CAGTT-C", "submitter": "3billion", "submitted_assembly": "GRCh37", "submitter_date": "2022-03-25"}, "clinvar_accession": {"acc": "SCV002318897", "version": 1, "type": "SCV", "date_updated": "2022-04-02", "date_created": "2022-04-02", "org_id": "507830", "org_type": "primary", "org_category": "other"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "14961560"}]}, {"ids": [{"source": "PubMed", "value": "20417570"}]}, {"ids": [{"source": "PubMed", "value": "11017079"}]}], "comments": [{"text": "Canonical splice site: predicted to alter splicing and result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 20417570, 14961560). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline."}], "date_last_evaluated": "2022-03-22"}], "external_ids": [{"db": "3billion", "id": "20220322091"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "number_tested": 1, "proband": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "SingleHeterozygote", "integer_value": 1}}], "traits": {"type": "Finding", "traits": [{"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000729"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0008499"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0001270"}]}, {"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0004322"}]}]}}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_130837.3:c.2873_2876del"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}]}}, {"id": 5041270, "submission_id": {"local_key": "NM_130837.3:c.2873-2_2874del|OMIM:165500", "submitter": "MGZ Medical Genetics Center", "submitted_assembly": "GRCh37", "submitter_date": "2022-10-06"}, "clinvar_accession": {"acc": "SCV002579707", "version": 1, "type": "SCV", "date_updated": "2022-10-15", "date_created": "2022-10-15", "org_id": "255845", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2021-11-26"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "gender": "male"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_130837.3:c.2873-2_2874del"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}], "xrefs": [{"db": "dbSNP", "id": "80356530", "type": "rsNumber"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}]}, "comments": [{"text": "ACMG criteria applied: PVS1, PS4, PM2_SUP"}]}, {"id": 7543925, "submission_id": {"local_key": "4093778_NM_130837.3:c.2873_2876del|OMIM:165500", "submitter": "Institute of Human Genetics, University of Leipzig Medical Center", "submitted_assembly": "GRCh37", "submitter_date": "2023-09-04"}, "clinvar_accession": {"acc": "SCV004032248", "version": 1, "type": "SCV", "date_updated": "2023-09-09", "date_created": "2023-09-09", "org_id": "506086", "org_type": "primary", "org_category": "clinic"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "comments": [{"text": "Criteria applied: PVS1,PS4,PS3_MOD"}], "date_last_evaluated": "2023-08-23"}], "external_ids": [{"db": "Institute of Human Genetics", "id": "4093778_NM_130837.3:c.2873_2876del"}], "attributes": [{"attribute": {"type": "ModeOfInheritance", "value": "Autosomal dominant inheritance"}}, {"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "gender": "male"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}], "traits": {"type": "Finding", "traits": [{"type": "Finding", "xrefs": [{"db": "HP", "id": "HP:0000648"}]}]}}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_130837.3:c.2873_2876del"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}]}}, {"id": 7569492, "submission_id": {"local_key": "168-20230924", "submitter": "Institute of Human Genetics, Klinikum rechts der Isar", "submitter_date": "2023-10-19"}, "clinvar_accession": {"acc": "SCV004045808", "version": 1, "type": "SCV", "date_updated": "2023-10-21", "date_created": "2023-10-21", "org_id": "500240", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2023-08-17"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Classification criteria August 2017"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/inodbbrd/classification_criteria.pdf"}]}, {"attribute": {"type": "ModeOfInheritance", "value": "Autosomal dominant inheritance"}}], "observed_in": [{"sample": {"origin": "maternal", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}], "traits": {"type": "Disease", "traits": [{"type": "Disease", "xrefs": [{"db": "HP", "id": "HP:0000648"}]}, {"type": "Disease", "xrefs": [{"db": "HP", "id": "HP:0000750"}]}]}}], "measures": {"type": "Variant", "measures": [{"type": "variation", "sequence_locations": [{"assembly": "GRCh37", "chr": "3", "start": 193384956, "stop": 193384960, "reference_allele": "CAGTT", "alternate_allele": "C"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "OPA1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "165500", "type": "MIM"}]}]}}]} -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000007528", "version": 47, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2013-04-04"}, "record_status": "current", "clinical_significance": {"review_status": "practice guideline", "description": "pathogenic", "date_last_evaluated": "2004-03-03"}, "assertion": "variation to disease", "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 2}}]}, {"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "no"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}]}, {"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "not provided"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "In 2 presumably unrelated families with mild cystic fibrosis (CF; 219700), Dean et al. (1990) found a 482G-A transition in exon 4 of the CFTR gene, resulting in an arg117-to-his (R117H) substitution."}, "citations": [{"ids": [{"source": "PubMed", "value": "1937486"}], "type": "general"}]}, {"attribute": {"type": "Description", "value": "Gervais et al. (1993) reported that the R117H mutation was present in 4 of 23 patients with congenital absence of the vas deferens (CBAVD; 277180). Three patients had compound heterozygosity for R117H and delF508 (602421.0001), whereas a fourth was a compound heterozygote for R117H and 2322delG. None of the 23 patients had pulmonary evidence of cystic fibrosis. Five patients without the delF508 mutation had unilateral renal agenesis in addition to absence of the vas deferens; these patients may represent a different distinct subset. Bienvenu et al. (1993) described for the first time homozygosity for the R117H mutation in a 30-year-old French male with sterility owing to congenital bilateral absence of the vas deferens. The subject had no respiratory or pancreatic involvement and had a normal sweat electrolyte value. His parents were not consanguineous, and there were no other cases of CBAVD or CF in the family."}, "citations": [{"ids": [{"source": "PubMed", "value": "7692051"}], "type": "general"}, {"ids": [{"source": "PubMed", "value": "8421472"}], "type": "general"}]}, {"attribute": {"type": "Description", "value": "Kiesewetter et al. (1993) presented evidence that the chromosome background of the R117H mutation has a profound effect on the phenotype produced. Three length variants of CFTR have been observed with varying degrees of exon 9 splicing depending on variation in the length of the polypyrimidine tract in the splice acceptor site in intron 8 (Chu et al., 1991, 1993). Varied lengths of a thymidine (T)-tract (5, 7, or 9Ts) were noted in front of the splice acceptor site of intron 8. The 5T variant is present in 5% of the CFTR alleles among Caucasian populations producing almost exclusively (95%) exon 9-minus RNA. The effect of this T-tract polymorphism in CFTR gene expression was also documented by its relationship with the R117H mutation: R117H (5T) is found in typical CF patients with pancreatic sufficiency; R117H (7T) is associated with CBAVD. The R117H mutation has been reported in CF patients, males with congenital bilateral absence of the vas deferens, and in an asymptomatic woman. Furthermore, population screening discovered a 19-fold higher than expected number of carriers of this CF mutation. The situation was compared to that in Gaucher disease in which the severity of neuronopathic disease associated with a missense mutation appears to be altered by additional missense mutations in the same allele (Latham et al., 1990)."}, "citations": [{"ids": [{"source": "PubMed", "value": "2349952"}], "type": "general"}, {"ids": [{"source": "PubMed", "value": "7506096"}], "type": "general"}]}, {"attribute": {"type": "Description", "value": "White et al. (2001) reported a healthy 29-year-old female who was found to be an R117H/delF508 heterozygote. The patient had atopic asthma and infertility, but normal height and weight and no pulmonary symptoms of CF. Analysis of the polythymidine tract showed that the R117H mutation was in cis with a 7T tract and the delta-F508 mutation in cis with a 9T tract. The authors concluded that poly-T studies are important in any patient found to have the R117H mutation, and recommended caution in the genetic counseling of such families."}, "citations": [{"ids": [{"source": "PubMed", "value": "11746017"}], "type": "general"}]}, {"attribute": {"type": "Description", "value": "Thauvin-Robinet et al. (2009) reported the results of a national collaborative study in France to establish the overall phenotype associated with R117H and to evaluate the disease penetrance of the R117H+F508del genotype. In 184 R117H+F508del individuals of the French population, including 72 newborns, the disease phenotype was predominantly mild; 1 child had classic cystic fibrosis, and 3 adults had severe pulmonary symptoms. In 5,245 healthy adults with no family history of CF, the allelic prevalence of F508del was 1.06%, R117H;T7 0.27%, and R117H;T5 less than 0.01%. The theoretical number of R117H;T7+F508del individuals in the French populations was estimated at 3650, whereas only 112 were known with CF related symptoms (3.1%). The penetrance of classic CF for R117H;T7+F508del was estimated at 0.03% and that of severe CF in adulthood at 0.06%. Thauvin-Robinet et al. (2009) suggested that R117H should be withdrawn from CF mutation panels used for screening programs."}, "citations": [{"ids": [{"source": "PubMed", "value": "19880712"}], "type": "general"}]}]}, {"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["clinical testing", "curation"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}]}, {"sample": {"origin": "maternal", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "NumFamiliesWithVariant", "integer_value": 1}}, {"attribute": {"type": "CompoundHeterozygote", "integer_value": 1}}]}, {"sample": {"origin": "maternal", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["research"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "SampleLocalID", "value": "7:117171029:G:00067C"}}]}, {"sample": {"origin": "paternal", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["research"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "SampleLocalID", "value": "7:117171029:G:00170C"}}]}, {"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing", "curation"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "Description", "value": "not provided"}}]}, {"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 3}, "methods": ["clinical testing", "literature only", "research"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 3}}, {"attribute": {"type": "SampleLocalID", "value": "7:117171029:G:00067M"}}, {"attribute": {"type": "SampleLocalID", "value": "7:117171029:G:00170D"}}, {"attribute": {"type": "SampleLocalID", "value": "7:117171029:G:00170"}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "acc": "VCV000007109", "version": 140, "measures": [{"type": "single nucleotide variant", "names": [{"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}], "canonical_spdi": "NC_000007.14:117530974:G:A", "attributes": [{"type": "HGVS, coding, LRG", "value": "LRG_663t1:c.350G>A"}, {"type": "HGVS, coding, RefSeq", "value": "NM_000492.4:c.350G>A"}, {"type": "HGVS, genomic, LRG", "value": "LRG_663:g.70192G>A"}, {"type": "HGVS, genomic, RefSeqGene", "value": "NG_016465.4:g.70192G>A"}, {"type": "HGVS, genomic, top level", "value": "NC_000007.14:g.117530975G>A", "integer_value": 38}, {"type": "HGVS, genomic, top level, previous", "value": "NC_000007.13:g.117171029G>A", "integer_value": 37}, {"type": "HGVS, previous", "value": "NM_000492.3:c.350G>A"}, {"type": "HGVS, protein"}, {"type": "HGVS, protein", "value": "LRG_663p1:p.Arg117His"}, {"type": "HGVS, protein", "value": "P13569:p.Arg117His"}, {"type": "HGVS, protein, RefSeq", "value": "NP_000483.3:p.Arg117His"}, {"type": "HGVS, protein, RefSeq", "value": "NP_000483.3:p.Arg117His"}, {"type": "Location", "value": "NM_000492.3:exon 4", "xrefs": [{"db": "HGMD", "id": "CM900043"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_000492.4:c.350G>A"}]}, {"type": "ProteinChange1LetterCode", "value": "R117H"}, {"type": "ProteinChange3LetterCode", "value": "ARG117HIS"}], "cytogenic_locations": ["7q31.2"], "sequence_locations": [{"assembly": "GRCh38", "chr": "7", "accession": "NC_000007.14", "start": 117530975, "stop": 117530975, "display_start": 117530975, "display_stop": 117530975, "variant_length": 1, "assembly_accession_version": "GCF_000001405.38", "assembly_status": "current", "position_vcf": 117530975, "reference_allele_vcf": "G", "alternate_allele_vcf": "A"}, {"assembly": "GRCh37", "chr": "7", "accession": "NC_000007.13", "start": 117171029, "stop": 117171029, "display_start": 117171029, "display_stop": 117171029, "variant_length": 1, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous", "position_vcf": 117171029, "reference_allele_vcf": "G", "alternate_allele_vcf": "A"}], "measure_relationship": [{"type": "within single gene", "names": [{"value": {"type": "Preferred", "value": "CF transmembrane conductance regulator"}}], "symbols": [{"value": {"type": "Preferred", "value": "CFTR"}}], "sequence_locations": [{"assembly": "GRCh38", "chr": "7", "accession": "NC_000007.14", "start": 117480025, "stop": 117668665, "display_start": 117480025, "display_stop": 117668665, "strand": "+", "assembly_accession_version": "GCF_000001405.38", "assembly_status": "current"}, {"assembly": "GRCh37", "chr": "7", "accession": "NC_000007.13", "start": 117120016, "stop": 117308718, "display_start": 117120016, "display_stop": 117308718, "strand": "+", "variant_length": 188703, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous"}], "xrefs": [{"db": "Gene", "id": "1080"}, {"db": "OMIM", "id": "602421", "type": "MIM"}, {"db": "HGNC", "id": "HGNC:1884"}]}], "citations": [{"ids": [{"source": "PubMed", "value": "11280952"}], "type": "general", "abbrev": "ACMG/ACOG, 2001"}, {"ids": [{"source": "pmc", "value": "3110945"}], "type": "general", "abbrev": "ACMG, 2004"}], "xrefs": [{"db": "CFTR-France", "id": "c.350G>A"}, {"db": "CFTR2", "id": "219"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000074114"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000257096"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000500233"}, {"db": "HGMD", "id": "CM900043"}, {"db": "Illumina Laboratory Services, Illumina", "id": "560651"}, {"db": "PharmGKB", "id": "1447964187"}, {"db": "PharmGKB", "id": "1447964187PA165950341"}, {"db": "Quest Diagnostics Nichols Institute San Juan Capistrano", "id": "2640108"}, {"db": "UniProtKB", "id": "P13569#VAR_000122"}, {"db": "OMIM", "id": "602421.0005", "type": "Allelic variant"}, {"db": "dbSNP", "id": "78655421", "type": "rs"}], "id": 22148}], "names": [{"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}, {"value": {"type": "Preferred", "value": "NM_000492.4(CFTR):c.350G>A (p.Arg117His)"}}], "xrefs": [{"db": "ClinGen", "id": "CA221026"}], "id": 7109}, "traits": {"type": "Disease", "traits": [{"type": "Disease", "names": [{"value": {"type": "Preferred", "value": "Cystic fibrosis"}, "xrefs": [{"db": "Genetic Alliance", "id": "Cystic+Fibrosis/2071"}, {"db": "MONDO", "id": "MONDO:0009061"}, {"db": "OMIM", "id": "219700", "type": "MIM"}, {"db": "SNOMED CT", "id": "190905008"}]}, {"value": {"type": "Alternate", "value": "Mucoviscidosis"}}], "symbols": [{"value": {"type": "Preferred", "value": "CF"}, "xrefs": [{"db": "OMIM", "id": "219700", "type": "MIM"}]}], "attributes": [{"value": {"type": "public definition", "value": "Cystic fibrosis (CF) is a multisystem disease affecting epithelia of the respiratory tract, exocrine pancreas, intestine, hepatobiliary system, and exocrine sweat glands. Morbidities include recurrent sinusitis and bronchitis, progressive obstructive pulmonary disease with bronchiectasis, exocrine pancreatic deficiency and malnutrition, pancreatitis, gastrointestinal manifestations (meconium ileus, rectal prolapse, distal intestinal obstructive syndrome), liver disease, diabetes, male infertility due to hypoplasia or aplasia of the vas deferens, and reduced fertility or infertility in some women. Pulmonary disease is the major cause of morbidity and mortality in CF."}, "xrefs": [{"db": "GeneReviews", "id": "NBK1250"}]}, {"value": {"type": "disease mechanism", "value": "loss of function"}, "xrefs": [{"db": "Genetic Testing Registry (GTR)", "id": "GTR000004176"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000005248"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000025280"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000028916"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000074114"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000209428"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000226639"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000246717"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000277984"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000320929"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000328569"}, {"db": "Genetic Testing Registry (GTR)", "id": "GTR000330969"}, {"db": "Genetic Testing 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"abbrev": "ACMG ACT, 2012", "url": "https://www.acmg.net/PDFLibrary/CF-Mutation-not-R117H.pdf", "citation_text": "American College of Medical Genetics and Genomics Carrier Screening ACT Sheet, CFTR Mutations except R117H, Cystic Fibrosis (CF), 2012"}, {"type": "practice guideline", "abbrev": "ACMG ACT, 2012", "url": "https://www.acmg.net/PDFLibrary/CF-Mutation-R117H.pdf", "citation_text": "American College of Medical Genetics and Genomics Carrier Screening ACT Sheet, Cystic Fibrosis R117H, 2012"}, {"type": "practice guideline", "abbrev": "ACMG ACT, 2012", "url": "https://www.acmg.net/PDFLibrary/CF-No-Mutation.pdf", "citation_text": "American College of Medical Genetics and Genomics Carrier Screening ACT Sheet, No Mutations Detected by Carrier Screening, Cystic Fibrosis (CF), 2012"}], "xrefs": [{"db": "MONDO", "id": "MONDO:0009061"}, {"db": "MedGen", "id": "C0010674"}, {"db": "Orphanet", "id": "586"}, {"db": "OMIM", "id": "219700", "type": "MIM"}]}], "id": 1961}, "citations": [{"ids": [{"source": "PubMed", "value": "31508243"}], "type": "general"}], "date_created": "2013-04-04", "date_last_updated": "2023-12-09", "id": 65031}, "record_status": "current", "replaces": ["RCV000049303"], "title": "NM_000492.4(CFTR):c.350G>A (p.Arg117His) AND Cystic fibrosis", "clinvar_assertions": [{"id": 27729, "submission_id": {"local_key": "602421.0005_CYSTIC FIBROSIS", "submitter": "OMIM", "title": "CFTR, ARG117HIS_CYSTIC FIBROSIS", "submitter_date": "2018-04-09"}, "clinvar_accession": {"acc": "SCV000027729", "version": 3, "type": "SCV", "date_updated": "2017-12-26", "date_created": "2013-04-04", "org_id": "3", "org_type": "primary", "org_category": "resource"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "no assertion criteria provided", "descriptions": ["pathogenic"], "date_last_evaluated": "2009-11-01"}], "external_ids": [{"db": "OMIM", "id": "602421.0005", "type": "Allelic variant"}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human"}, "affected_status": "not provided"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "In 2 presumably unrelated families with mild cystic fibrosis (CF; 219700), Dean et al. (1990) found a 482G-A transition in exon 4 of the CFTR gene, resulting in an arg117-to-his (R117H) substitution."}, "citations": [{"ids": [{"source": "PubMed", "value": "1937486"}]}], "xrefs": [{"db": "OMIM", "id": "219700", "type": "MIM"}]}, {"attribute": {"type": "Description", "value": "Gervais et al. (1993) reported that the R117H mutation was present in 4 of 23 patients with congenital absence of the vas deferens (CBAVD; 277180). Three patients had compound heterozygosity for R117H and delF508 (602421.0001), whereas a fourth was a compound heterozygote for R117H and 2322delG. None of the 23 patients had pulmonary evidence of cystic fibrosis. Five patients without the delF508 mutation had unilateral renal agenesis in addition to absence of the vas deferens; these patients may represent a different distinct subset. Bienvenu et al. (1993) described for the first time homozygosity for the R117H mutation in a 30-year-old French male with sterility owing to congenital bilateral absence of the vas deferens. The subject had no respiratory or pancreatic involvement and had a normal sweat electrolyte value. His parents were not consanguineous, and there were no other cases of CBAVD or CF in the family."}, "citations": [{"ids": [{"source": "PubMed", "value": "8421472"}]}, {"ids": [{"source": "PubMed", "value": "7692051"}]}], "xrefs": [{"db": "OMIM", "id": "277180", "type": "MIM"}]}, {"attribute": {"type": "Description", "value": "Kiesewetter et al. (1993) presented evidence that the chromosome background of the R117H mutation has a profound effect on the phenotype produced. Three length variants of CFTR have been observed with varying degrees of exon 9 splicing depending on variation in the length of the polypyrimidine tract in the splice acceptor site in intron 8 (Chu et al., 1991, 1993). Varied lengths of a thymidine (T)-tract (5, 7, or 9Ts) were noted in front of the splice acceptor site of intron 8. The 5T variant is present in 5% of the CFTR alleles among Caucasian populations producing almost exclusively (95%) exon 9-minus RNA. The effect of this T-tract polymorphism in CFTR gene expression was also documented by its relationship with the R117H mutation: R117H (5T) is found in typical CF patients with pancreatic sufficiency; R117H (7T) is associated with CBAVD. The R117H mutation has been reported in CF patients, males with congenital bilateral absence of the vas deferens, and in an asymptomatic woman. Furthermore, population screening discovered a 19-fold higher than expected number of carriers of this CF mutation. The situation was compared to that in Gaucher disease in which the severity of neuronopathic disease associated with a missense mutation appears to be altered by additional missense mutations in the same allele (Latham et al., 1990)."}, "citations": [{"ids": [{"source": "PubMed", "value": "7506096"}]}, {"ids": [{"source": "PubMed", "value": "2349952"}]}]}, {"attribute": {"type": "Description", "value": "White et al. (2001) reported a healthy 29-year-old female who was found to be an R117H/delF508 heterozygote. The patient had atopic asthma and infertility, but normal height and weight and no pulmonary symptoms of CF. Analysis of the polythymidine tract showed that the R117H mutation was in cis with a 7T tract and the delta-F508 mutation in cis with a 9T tract. The authors concluded that poly-T studies are important in any patient found to have the R117H mutation, and recommended caution in the genetic counseling of such families."}, "citations": [{"ids": [{"source": "PubMed", "value": "11746017"}]}]}, {"attribute": {"type": "Description", "value": "Thauvin-Robinet et al. (2009) reported the results of a national collaborative study in France to establish the overall phenotype associated with R117H and to evaluate the disease penetrance of the R117H+F508del genotype. In 184 R117H+F508del individuals of the French population, including 72 newborns, the disease phenotype was predominantly mild; 1 child had classic cystic fibrosis, and 3 adults had severe pulmonary symptoms. In 5,245 healthy adults with no family history of CF, the allelic prevalence of F508del was 1.06%, R117H;T7 0.27%, and R117H;T5 less than 0.01%. The theoretical number of R117H;T7+F508del individuals in the French populations was estimated at 3650, whereas only 112 were known with CF related symptoms (3.1%). The penetrance of classic CF for R117H;T7+F508del was estimated at 0.03% and that of severe CF in adulthood at 0.06%. Thauvin-Robinet et al. (2009) suggested that R117H should be withdrawn from CF mutation panels used for screening programs."}, "citations": [{"ids": [{"source": "PubMed", "value": "19880712"}]}]}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "names": [{"value": {"type": "Preferred", "value": "CFTR, ARG117HIS"}}], "attributes": [{"type": "NonHGVS", "value": "ARG117HIS"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CFTR"}}]}], "xrefs": [{"db": "OMIM", "id": "602421.0005", "type": "Allelic variant"}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "CYSTIC FIBROSIS"}}]}]}}, {"id": 118593, "submission_id": {"local_key": "NM_000492.3:c.350G>A|OMIM:219700", "submitter": "American College of Medical Genetics and Genomics (ACMG)"}, "clinvar_accession": {"acc": "SCV000071404", "version": 2, "type": "SCV", "date_updated": "2014-02-06", "date_created": "2013-06-04", "org_id": "500073", "org_type": "primary", "org_category": "other"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "practice guideline", "descriptions": ["pathogenic"], "comments": [{"text": "Converted during submission to Pathogenic."}], "date_last_evaluated": "2004-03-03"}], "attributes": [{"attribute": {"type": "ModeOfInheritance", "value": "Autosomal recessive inheritance"}}, {"attribute": {"type": "AssertionMethod", "value": "Guideline for cystic fibrosis carrier screening"}, "citations": [{"ids": [{"source": "PubMed", "value": "11280952"}], "type": "practice guideline", "abbrev": "ACMG/ACOG, 2001"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["curation"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000492.3:c.350G>A"}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "Cystic fibrosis"}}], "xrefs": [{"db": "OMIM", "id": "219700"}]}]}, "citations": [{"ids": [{"source": "PubMed", "value": "11280952"}], "type": "practice guideline", "abbrev": "ACMG/ACOG, 2001"}, {"ids": [{"source": "pmc", "value": "3110945"}], "type": "practice guideline", "abbrev": "ACMG, 2004"}], "study_name": "The ACMG recommended carrier screening panel"}, {"id": 122860, "submission_id": {"local_key": "28027|MedGen:C0010674", "submitter": "Invitae", "submitted_assembly": "GRCh37", "submitter_date": "2023-01-10"}, "clinvar_accession": {"acc": "SCV000074930", "version": 11, "type": "SCV", "date_updated": "2023-02-07", "date_created": "2013-07-03", "org_id": "500031", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "flagged submission", "descriptions": ["uncertain significance"], "citations": [{"ids": [{"source": "PubMed", "value": "7506096"}]}, {"ids": [{"source": "PubMed", "value": "11491164"}]}, {"ids": [{"source": "PubMed", "value": "7691356"}]}, {"ids": [{"source": "PubMed", "value": "7684641"}]}, {"ids": [{"source": "PubMed", "value": "10556281"}]}, {"ids": [{"source": "PubMed", "value": "14685937"}]}, {"ids": [{"source": "PubMed", "value": "21658649"}]}, {"ids": [{"source": "PubMed", "value": "7506096"}]}, {"ids": [{"source": "PubMed", "value": "11491164"}]}, {"ids": [{"source": "PubMed", "value": "21507732"}]}, {"ids": [{"source": "PubMed", "value": "7506096"}]}, {"ids": [{"source": "PubMed", "value": "23974870"}]}, {"ids": [{"source": "PubMed", "value": "21507732"}]}, {"ids": [{"source": "PubMed", "value": "19880712"}]}, {"ids": [{"source": "PubMed", "value": "11242048"}]}, {"ids": [{"source": "PubMed", "value": "21507732"}]}], "comments": [{"text": "This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 117 of the CFTR protein (p.Arg117His). This variant is present in population databases (rs78655421, gnomAD 0.2%), including at least one homozygous and/or hemizygous individual. This missense variant (also known as R117H) frequently occurs on the same chromosome as a pathogenic CFTR allele known as IVS8-5T (PMID: 7506096, 11491164). The 5T refers to a polymorphic region in the intron preceding the acceptor splice site for exon 10 (formerly called exon 9). The 5T allele has been demonstrated to result in aberrant mRNA splicing and a non-functional protein, while more common 7T and 9T alleles do not impact splicing and are considered benign (PMID: 7691356, 7684641, 10556281, 14685937, 21658649). Importantly, when R117H is on the same chromosome as the 5T, it may increase the severity of CFTR-related symptoms (PMID: 7506096, 11491164). When on the same chromosome as a 7T or 9T, the R117H variant has not been associated with cystic fibrosis (PMID: 21507732, 7506096, 23974870). The R117H and T7 (R117H-T7) allele has been reported to be homozygous in a male with congenital absence of vas deferens (CAVD) (PMID: 21507732). This male also had slightly above normal sweat chloride levels (34 mmol/L) but was otherwise asymptomatic for CFTR-related symptoms. In addition, 81 males with R117H-T7 and Phe508del on opposite alleles have been observed to have CAVD, although it has been estimated that only a small percentage (3%) of males in the population with this genotype are affected (PMID: 19880712). ClinVar contains an entry for this variant (Variation ID: 7109). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CFTR protein function. The experimental evidence for the R117H-T7 is conflicting. In a heterologous model system, this missense change decreased CFTR activity by ~20-30% (PMID: 11242048), while in airway epithelium cells taken from two individuals homozygous for R117H-T7, chloride conductance levels were normal (PMID: 21507732). In summary, this R117H missense variant may modify disease severity when it occurs on the same chromosome as a 5T allele. When present on the same chromosome as a 7T or 9T allele, the R117H variant does not contribute to cystic fibrosis but may contribute to CAVD. However, much of the functional and clinical data for the R117H-T7 allele is conflicting. Until this can be resolved, the R117H missense change has been classified as a Variant of Uncertain Significance."}], "date_last_evaluated": "2022-11-01"}], "external_ids": [{"db": "Invitae", "id": "28027"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Invitae Variant Classification Sherloc (09022015)"}, "citations": [{"ids": [{"source": "PubMed", "value": "28492532"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NC_000007.13:g.117171029G>A"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CFTR"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "MedGen", "id": "C0010674", "type": "CUI"}]}]}, "citations": [{"ids": [{"source": "PubMed", "value": "28492532"}], "type": "general"}], "comments": [{"text": "Notes: None", "type": "FlaggedComment", "datasource": "ClinGen"}, {"text": "Reason: Outlier claim with insufficient supporting evidence", "type": "FlaggedComment", "datasource": "ClinGen"}]}, {"id": 432841, "submission_id": {"local_key": "chr7@117171029|G|A|OMIM:219700", "submitter": "Courtagen Diagnostics Laboratory, Courtagen Life Sciences", "submitter_date": "2015-05-28"}, "clinvar_accession": {"acc": "SCV000236522", "version": 2, "type": "SCV", "date_updated": "2015-07-05", "date_created": "2015-07-05", "org_id": "320384", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2014-04-23"}], "external_ids": [{"db": "Courtagen Life Sciences", "id": "chr7@117171029|G|A"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Courtagen Life Sciences Classifications"}, "citations": [{"type": "general", "url": "https://submit.ncbi.nlm.nih.gov/ft/byid/k97lr6ce/mdi-5595-320384_courtagen_life_sciences_classification_definitions_final.docx"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000492.3:c.350G>A"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CFTR"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "Cystic fibrosis"}}], "xrefs": [{"db": "OMIM", "id": "219700", "type": "MIM"}]}]}}, {"id": 1139206, "submission_id": {"local_key": "7:117171029:G", "submitter": "HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology", "submitted_assembly": "GRCh37", "submitter_date": "2017-07-06"}, "clinvar_accession": {"acc": "SCV000584076", "version": 1, "type": "SCV", "date_updated": "2015-10-11", "date_created": "2015-10-11", "org_id": "505530", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["likely pathogenic"], "date_last_evaluated": "2014-11-04"}], "external_ids": [{"db": "HudsonAlpha Institute for Biotechnology", "id": "7:117171029"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "HA_assertions_20150911"}, "citations": [{"type": "general", "url": "https://submit.ncbi.nlm.nih.gov/ft/byid/zo9ynrar/ha_assertions_20150911.pdf", "citation_text": "HA_assertions_20150911.pdf"}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["research"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "SampleLocalID", "value": "7:117171029:G:00067M"}}]}, {"sample": {"origin": "maternal", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["research"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "SampleLocalID", "value": "7:117171029:G:00067C"}}]}, {"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["research"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "SampleLocalID", "value": "7:117171029:G:00170D"}}]}, {"sample": {"origin": "paternal", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["research"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "SampleLocalID", "value": "7:117171029:G:00170C"}}]}, {"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["research"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "SampleLocalID", "value": "7:117171029:G:00170"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "sequence_locations": [{"assembly": "GRCh37", "chr": "7", "start": 117171029, "stop": 117171029, "variant_length": 1, "reference_allele": "G", "alternate_allele": "A"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CFTR"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "219700", "type": "MIM"}]}]}, "study_name": "CSER-HudsonAlpha"}, {"id": 1363325, "submission_id": {"local_key": "NM_000492.3:c.350G>A|MedGen:C0010674", "submitter": "Women's Health and Genetics/Laboratory Corporation of America, LabCorp", "submitted_assembly": "GRCh37", "submitter_date": "2018-01-25"}, "clinvar_accession": {"acc": "SCV000696973", "version": 1, "type": "SCV", "date_updated": "2017-12-26", "date_created": "2017-12-26", "org_id": "500026", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "10341008"}]}, {"ids": [{"source": "PubMed", "value": "7692051"}]}, {"ids": [{"source": "PubMed", "value": "12767731"}]}, {"ids": [{"source": "PubMed", "value": "7599637"}]}, {"ids": [{"source": "PubMed", "value": "7522329"}]}, {"ids": [{"source": "PubMed", "value": "10653141"}]}, {"ids": [{"source": "PubMed", "value": "9259197"}]}, {"ids": [{"source": "PubMed", "value": "7573058"}]}, {"ids": [{"source": "PubMed", "value": "8698344"}]}, {"ids": [{"source": "PubMed", "value": "15246977"}]}, {"ids": [{"source": "PubMed", "value": "11737931"}]}, {"ids": [{"source": "PubMed", "value": "17015492"}]}, {"ids": [{"source": "PubMed", "value": "7506096"}]}, {"ids": [{"source": "PubMed", "value": "19092437"}]}, {"ids": [{"source": "PubMed", "value": "9272157"}]}, {"ids": [{"source": "PubMed", "value": "7680769"}]}, {"ids": [{"source": "PubMed", "value": "9557894"}]}, {"ids": [{"source": "PubMed", "value": "9950763"}]}, {"ids": [{"source": "PubMed", "value": "9259194"}]}, {"ids": [{"source": "PubMed", "value": "10103316"}]}, {"ids": [{"source": "PubMed", "value": "11168024"}]}, {"ids": [{"source": "PubMed", "value": "1283148"}]}, {"ids": [{"source": "PubMed", "value": "10909845"}]}, {"ids": [{"source": "PubMed", "value": "8825927"}]}, {"ids": [{"source": "PubMed", "value": "7544788"}]}, {"ids": [{"source": "PubMed", "value": "23974870"}]}, {"ids": [{"source": "PubMed", "value": "9550361"}]}], "comments": [{"text": "Variant summary: The variant of interest causes a missense change involving a conserved nucleotide with 5/5 in silico programs predicting a \"deleterious\" outcome. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 185/120360 (1/650), which does not exceed the predicted maximum expected allele frequency for a pathogenic CFTR variant of 1/100. The variant of interest has been reported in multiple affected individuals via publications and databases that indicate that the variant of interest is a common disease variant with varying severity dependent on additional CFTR variants in cis and trans. Functional studies indicate that the variant of interest impedes wild type function. In addition, multiple reputable clinical laboratories cite the variant with a classification of \"pathogenic.\" Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Pathogenic."}], "date_last_evaluated": "2016-04-11"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "LabCorp Variant Classification Summary - May 2015"}, "citations": [{"type": "general", "url": "https://submit.ncbi.nlm.nih.gov/ft/byid/rtxspsnt/labcorp_variant_classification_method_-_may_2015.pdf", "citation_text": "LabCorp Variant Classification Summary - May 2015.docx"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000492.3:c.350G>A"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CFTR"}}]}], "xrefs": [{"db": "dbSNP", "id": "78655421", "type": "rsNumber"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "MedGen", "id": "C0010674", "type": "CUI"}]}]}}, {"id": 1732919, "submission_id": {"local_key": "NC_000007.13:g.117171029G>A|OMIM:219700", "submitter": "Mendelics", "submitted_assembly": "GRCh37", "submitter_date": "2018-11-11"}, "clinvar_accession": {"acc": "SCV000886267", "version": 2, "type": "SCV", "date_updated": "2022-12-11", "date_created": "2018-10-10", "org_id": "500035", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2018-11-05"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Mendelics Assertion Criteria 2017"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/chhjzatu/mendelics_assertion_criteria_2017.pdf"}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NC_000007.13:g.117171029G>A"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CFTR"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "219700", "type": "MIM"}]}]}}, {"id": 1791253, "submission_id": {"local_key": "801449", "submitter": "Illumina Laboratory Services, Illumina", "submitted_assembly": "GRCh37", "submitter_date": "2019-02-01"}, "clinvar_accession": {"acc": "SCV000916176", "version": 1, "type": "SCV", "date_updated": "2019-05-27", "date_created": "2019-05-27", "org_id": "504895", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "11280952"}]}, {"ids": [{"source": "PubMed", "value": "7506096"}]}, {"ids": [{"source": "PubMed", "value": "11491164"}]}, {"ids": [{"source": "PubMed", "value": "23974870"}]}], "comments": [{"text": "The CFTR c.350G>A (p.Arg117His) variant is included within the American College of Medical Genetics and Genomics (ACMG) recommended carrier screening panel for cystic fibrosis (Grody et al. 2001). There are multiple clinical implications for the p.Arg117His variant that are dependent on the length of the intron 8 polythymidine tract (polyT) region within the CFTR gene. Kiesewetter et al. (1993) and Massie et al. (2001) assessed the influence of the intron-8 polythymidine sequence (IVS8) on the relationship between the genotype and phenotype of individuals with the p.Arg117His variant. They found that when the p.Arg117His variant was found in cis with five thymidines (5T), and in trans to a pathogenic CF variant, the individual was most commonly affected with classic CF. When the p.Arg117His variant was identified in cis with seven thymidines (7T) and in trans to a pathogenic CF variant, male individuals were often affected with congenital absence of the vas deferens (CAVD), and males and females often presented with a milder variation of CF. In the CFTR2 database, the variant was found in 793 CF patients (808 alleles) and was classified as a mutation of varying clinical consequence (Sosnay et al. 2013). The p.Arg117His variant is reported at a frequency of 0.00256 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the collective evidence, the p.Arg117His variant is classified as pathogenic for CFTR-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population."}], "date_last_evaluated": "2017-04-27"}], "external_ids": [{"db": "Illumina Clinical Services Laboratory", "id": "560651"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ICSL Variant Classification Criteria 09 May 2019"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/thsgk7t4/icsl_variant_classification_criteria_09_may_2019.pdf"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000492.3:c.350G>A"}], "sequence_locations": [{"assembly": "GRCh37", "chr": "7", "start": 117171029, "stop": 117171029, "variant_length": 1, "reference_allele": "G", "alternate_allele": "A"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CFTR"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "CFTR-Related Disorders"}}]}]}}, {"id": 2321961, "submission_id": {"local_key": "a5654", "submitter": "Ambry Genetics", "submitted_assembly": "GRCh37", "submitter_date": "2022-11-11"}, "clinvar_accession": {"acc": "SCV001181971", "version": 3, "type": "SCV", "date_updated": "2022-11-29", "date_created": "2020-03-16", "org_id": "61756", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "23378603"}]}, {"ids": [{"source": "PubMed", "value": "26846474"}]}, {"ids": [{"source": "PubMed", "value": "27469177"}]}], "comments": [{"text": "The p.R117H pathogenic mutation (also known as c.350G>A), located in coding exon 4 of the CFTR gene, results from a G to A substitution at nucleotide position 350. The arginine at codon 117 is replaced by histidine, an amino acid with highly similar properties. The penetrance of the p.R117H mutation is modified by the poly-thymidine tract in CFTR intron 9; decreasing length of the poly-thymidine tract correlates with an increased risk for cystic fibrosis phenotype. When p.R117H is on the same chromosome as 5T (in cis) it is a disease causing mutation; when in cis with 7T, the allele acts as a variant of varying clinical consequence (VVCC) (Sosnay PR et al. Nat. Genet. 2013 Oct; 45(10):1160-7; Sosnay PR et al. Pediatr. Clin. North Am. 2016 Aug;63(4):585-98). In a study of 179 individuals who were compound heterozygous for p.R117H and another pathogenic CFTR mutation, 172 had poly-thymidine variant results documented, with the majority being 7T and only five individuals carrying the 5T allele. Clinical data were available for 166 individuals and diagnoses included: isolated CBAVD (83 individuals), CFTR-related disorder with mild or absent pulmonary disease (67 individuals), late-onset marked pulmonary disease (4 individuals), and asymptomatic (12 individuals) (Thauvin-Robinet C et al. J. Med. Genet., 2013 Apr;50:220-7). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation."}], "date_last_evaluated": "2021-10-07"}], "external_ids": [{"db": "Ambry Genetics", "id": "a5654"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Ambry General Variant Classification Scheme_2022"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/5hsvndk6/ambry_general_variant_classification_scheme_2022.pdf"}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "number_tested": 1}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000492.3:c.350G>A"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CFTR"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "MedGen", "id": "C0010674", "type": "CUI"}]}]}}, {"id": 2354257, "submission_id": {"local_key": "117|OMIM:219700", "submitter": "Myriad Genetics, Inc.", "submitted_assembly": "GRCh37", "submitter_date": "2020-06-18"}, "clinvar_accession": {"acc": "SCV001193802", "version": 2, "type": "SCV", "date_updated": "2020-07-06", "date_created": "2020-04-06", "org_id": "507240", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "replaced_list": [{"accession": "SCV000485158", "version": 2, "date_changed": "2020-07-02"}], "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "23974870"}]}, {"ids": [{"source": "PubMed", "value": "15371902"}]}], "comments": [{"text": "NM_000492.3(CFTR):c.350G>A(R117H) is classified as pathogenic in the context of cystic fibrosis. Please note that the R117H mutation is associated with a broad spectrum of disease, ranging from clinically asymptomatic to CAVD/non-classic cystic fibrosis. Individuals with R117H should have testing for the poly-T tract (5T) to determine accurate risk. Individuals with R117H and 5T in cis are at highest risk for CF symptoms. In the absence of the 5T haplotype, the R117H mutation is unlikely to produce significant symptoms of cystic fibrosis. The R117H mutation in combination with another disease causing mutation may result in borderline or elevated sweat chloride and mild clinical symptoms of CF, including male infertility. Sources used for classification include PMID 23974870 and 15371902. In summary, classification of NM_000492.3(CFTR):c.350G>A(R117H) is based on the following criteria: high frequency variant with variable penetrance and variable severity dependent on the presence of other variants in the gene. Please note: this variant was assessed in the context of healthy population screening."}], "date_last_evaluated": "2019-10-18"}], "external_ids": [{"db": "Myriad Women's Health, Inc.", "id": "117"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019)"}, "citations": [{"url": "https://submit.ncbi.nlm.nih.gov/ft/byid/vlxza0ea/myriad_women_s_health_autosomal_recessive_and_x-linked_classification_criteria_2019_.pdf"}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "sequence_locations": [{"assembly": "GRCh37", "chr": "7", "start": 117171029, "stop": 117171029, "variant_length": 1, "reference_allele": "G", "alternate_allele": "A"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "CFTR"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "219700", "type": "MIM"}]}]}}, {"id": 2998499, "submission_id": {"local_key": "21189|OMIM:219700", "submitter": "Baylor Genetics", "submitted_assembly": "GRCh38", "submitter_date": "2023-10-02"}, "clinvar_accession": {"acc": "SCV001523284", "version": 2, "type": "SCV", "date_updated": "2023-03-11", "date_created": "2021-03-22", "org_id": "1006", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "date_last_evaluated": "2023-01-27"}], "external_ids": [{"db": "Baylor Genetics", "id": "21189"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "ACMG Guidelines, 2015"}, "citations": [{"ids": [{"source": "PubMed", "value": "25741868"}]}]}], "observed_in": [{"sample": {"origin": "unknown", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_000492.4:c.350G>A"}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "219700", "type": "MIM"}]}]}}, {"id": 3194090, "submission_id": {"local_key": "NM_000492.3:c.350G>A|OMIM:219700", "submitter": "GeneReviews", "submitted_assembly": "not applicable", "submitter_date": "2021-05-21"}, "clinvar_accession": {"acc": "SCV001622784", "version": 2, "type": "SCV", "date_updated": "2022-10-01", "date_created": "2021-05-23", "org_id": "500062", "org_type": "primary", "org_category": "resource"}, "assertion_type": "variation to disease", 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"traits": [{"xrefs": [{"db": "OMIM", "id": "248200", "type": "MIM"}]}]}, "study_description": "Variants as described in Haer-Wigman et al. 2016", "comments": [{"text": "Reason: This record appears to be redundant with a more recent record from the same submitter.", "type": "FlaggedComment", "datasource": "NCBI"}, {"text": "Notes: SCV000804586 appears to be redundant with SCV001951631.", "type": "FlaggedComment", "datasource": "NCBI"}]}, {"id": 3047383, "submission_id": {"local_key": "NM_000350.2:c.634C>T|OMIM:248200", "submitter": "Institute of Medical Molecular Genetics, University of Zurich", "submitted_assembly": "GRCh37", "submitter_date": "2021-03-19"}, "clinvar_accession": {"acc": "SCV001548033", "version": 1, "type": "SCV", "date_updated": "2021-03-28", "date_created": "2021-03-28", "org_id": "300471", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria 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"33546218"}], "type": "general"}]}, {"id": 4538635, "submission_id": {"local_key": "1-94564484-G-A", "submitter": "3billion", "submitted_assembly": "GRCh37", "submitter_date": "2022-03-25"}, "clinvar_accession": {"acc": "SCV002318863", "version": 1, "type": "SCV", "date_updated": "2022-04-02", "date_created": "2022-04-02", "org_id": "507830", "org_type": "primary", "org_category": "other"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "criteria provided, single submitter", "descriptions": ["pathogenic"], "citations": [{"ids": [{"source": "PubMed", "value": "10711710"}]}, {"ids": [{"source": "PubMed", "value": "26161775"}]}, {"ids": [{"source": "PubMed", "value": "30093795"}]}, {"ids": [{"source": "PubMed", "value": "29925512"}]}, {"ids": [{"source": "PubMed", "value": "9503029"}]}], "comments": [{"text": "Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000007898, PMID:9503029). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 4 similarly affected unrelated individuals (PMID: 29925512, 30093795, 26161775) and it has been co-segregated with Stargardt disease 1 in multiple affected family members (PMID: 10711710). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.847>=0.6, 3CNET: 0.973>=0.75). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.0001195). 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(2000) reported the same mutation in a North American patient."}, "citations": [{"ids": [{"source": "PubMed", "value": "9697692"}]}, {"ids": [{"source": "PubMed", "value": "10937588"}]}], "xrefs": [{"db": "OMIM", "id": "312600", "type": "MIM"}]}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "names": [{"value": {"type": "Preferred", "value": "RP2, ARG118HIS"}}], "attributes": [{"type": "NonHGVS", "value": "ARG118HIS"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "RP2"}}]}], "xrefs": [{"db": "OMIM", "id": "300757.0003", "type": "Allelic variant"}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "RETINITIS PIGMENTOSA 2"}}]}]}}, {"id": 1569375, "submission_id": {"local_key": "NM_006915.2:c.353G>A|OMIM:312600", "submitter": "Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+", "submitted_assembly": "GRCh37", "submitter_date": "2016-09-14"}, "clinvar_accession": {"acc": "SCV000804699", "version": 2, "type": "SCV", "date_updated": "2018-09-10", "date_created": "2018-09-10", "org_id": "505925", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "flagged submission", "descriptions": ["pathogenic"], "date_last_evaluated": "2016-09-01"}], "observed_in": [{"sample": {"origin": "inherited", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 1}}, {"attribute": {"type": "VariantChromosomes", "integer_value": 1}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_006915.2:c.353G>A"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "RP2"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"xrefs": [{"db": "OMIM", "id": "312600", "type": "MIM"}]}]}, "study_description": "Variants as described in Haer-Wigman et al. 2016", "comments": [{"text": "Reason: This record appears to be redundant with a more recent record from the same submitter.", "type": "FlaggedComment", "datasource": "NCBI"}, {"text": "Notes: SCV000804699 appears to be redundant with SCV001959522.", "type": "FlaggedComment", "datasource": "NCBI"}]}]} -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000012831", "version": 12, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2013-04-04"}, "record_status": "current", "clinical_significance": {"review_status": "criteria provided, single submitter", "description": "pathogenic", "date_last_evaluated": "2016-10-14"}, "assertion": "variation to disease", "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["clinical testing", "curation"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}, {"attribute": {"type": "Description", "value": "not provided"}}]}, {"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "not provided"}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "In affected members of 2 unrelated but consanguineous families of Arabian ancestry with Fanconi anemia of complementation group C (FANCC; 227645), Hartmann et al. 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Auerbach. Submitter to LOVD: Arleen D. 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This variant occurs in the invariant region (+/- 1/2) of the splice consensus sequence and is predicted to cause altered splicing leading to an abnormal or absent protein. Functional analysis using fibroblasts from patients with this variant revealed aberrant mRNA processing however correct splicing was still observed at very low levels which might contribute to the milder clinical manifestations of the disease in patients with this variant (PMID: 20869034). In summary this variant meets our criteria to be classified as pathogenic."}, {"text": "Reason: This record appears to be redundant with a more recent record from the same submitter.", "type": "FlaggedComment", "datasource": "NCBI"}, {"text": "Notes: SCV001984200 appears to be redundant with SCV002818196.", "type": "FlaggedComment", "datasource": "NCBI"}]}]} +{"accession": {"accession": "VCV000004255", "version": 42}, "rcvs": [{"accession": {"accession": "RCV000004477", "version": 35}, "title": "NM_000784.4(CYP27A1):c.1183C>T (p.Arg395Cys) AND Cholestanol storage disease"}, {"accession": {"accession": "RCV000275162", "version": 18}, "title": "NM_000784.4(CYP27A1):c.1183C>T (p.Arg395Cys) AND not provided"}, {"accession": {"accession": "RCV001252460", "version": 2}, "title": "NM_000784.4(CYP27A1):c.1183C>T (p.Arg395Cys) AND Intellectual disability"}, {"accession": {"accession": "RCV003974793", "version": 1}, "title": "NM_000784.4(CYP27A1):c.1183C>T (p.Arg395Cys) AND CYP27A1-related condition"}], "name": "NM_000784.4(CYP27A1):c.1183C>T (p.Arg395Cys)", "variationType": "VARIATION_TYPE_SNV", "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS", "description": "Pathogenic/Likely pathogenic", "citations": [{"ids": [{"value": "25741868", "source": "PubMed"}, {"value": "4544753", "source": "pmc"}, {"value": "10.1038/gim.2015.30", "source": "DOI"}], "type": "general", "abbrev": "ACMG, 2015"}, {"ids": [{"value": "10775536", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "12933951", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "16157755", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "17697869", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "18227423", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "19092443", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "2019602", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "20402754", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "21073839", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "21645175", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "21955034", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "24002088", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "24746394", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "25862734", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "25983621", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "26156051", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "26906304", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "28324197", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "28894950", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "29260356", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "33659184", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "33977023", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "34234304", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "8950197", "source": "PubMed"}], "type": "general"}, {"ids": [{"value": "9790667", "source": "PubMed"}], "type": "general"}, {"url": "http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP27A1", "type": "general"}, {"ids": [{"value": "20301583", "source": "PubMed"}, {"value": "NBK1409", "source": "BookShelf"}], "type": "review", "abbrev": "GeneReviews"}], "conditions": [{"traits": [{"names": [{"value": "CYP27A1-related condition", "type": "Preferred"}]}], "type": "TYPE_DISEASE", "id": "89503", "contributesToAggregateClassification": true}, {"traits": [{"names": [{"value": "none provided", "type": "Alternate"}, {"value": "not provided", "type": "Preferred", "xrefs": [{"db": "Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre", "id": "13DG0619"}]}], "attributes": [{"attribute": {"base": {"value": "The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 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Visual acuity is usually stable over time; both nystagmus and sensitivity to bright light may improve slightly. Although the fundus is usually normal, macular changes (which may show early signs of progression) and vessel narrowing may be present in some affected individuals. 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11}}, "sequenceLocation": {"assembly": "GRCh37", "chr": "CHROMOSOME_2", "accession": "NC_000002.11", "start": 99012480, "stop": 99012480, "displayStart": 99012480, "displayStop": 99012480, "variantLength": 1, "positionVcf": 99012480, "referenceAlleleVcf": "C", "alternateAlleleVcf": "T"}, "hgncIds": ["HGNC:2150"]} diff --git a/tests/clinvar-minimal/clinvar-seqvars-grch37-no-unflagged.jsonl b/tests/clinvar-minimal/clinvar-seqvars-grch37-no-unflagged.jsonl index acb18796..19c3e5dd 100644 --- a/tests/clinvar-minimal/clinvar-seqvars-grch37-no-unflagged.jsonl +++ b/tests/clinvar-minimal/clinvar-seqvars-grch37-no-unflagged.jsonl @@ -1,10 +1,13 @@ -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000035198", "version": 6, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2013-05-03"}, "record_status": "current", "clinical_significance": {"review_status": "no classifications from unflagged records", "description": "other", "date_last_evaluated": "2023-04-14"}, 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"Preferred", "value": "not specified"}}]}]}, "comments": [{"text": "Notes: None", "type": "FlaggedComment", "datasource": "ClinGen"}, {"text": "Reason: Older claim that does not account for recent evidence", "type": "FlaggedComment", "datasource": "ClinGen"}]}]} -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000036357", "version": 9, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2013-05-03"}, "record_status": "current", "clinical_significance": {"review_status": "no classifications from unflagged records", "description": "other", "date_last_evaluated": "2023-04-14"}, "assertion": "variation to disease", "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 3}}, {"attribute": {"type": "NumFamiliesWithVariant", "integer_value": 1}}]}], "measures": {"type": "Variant", "acc": "VCV000043437", "version": 25, "measures": [{"type": "single nucleotide variant", "names": [{"value": {"type": "Preferred", "value": "NM_001018005.2(TPM1):c.725C>T (p.Ala242Val)"}}], "canonical_spdi": "NC_000015.10:63062597:C:T", "attributes": [{"type": "HGVS, coding, LRG", "value": "LRG_387t1:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001018008.2:c.617C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001301289.2:c.617C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001330344.2:c.617C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001330346.2:c.617C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001330351.2:c.617C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001365780.1:c.617C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001365781.2:c.617C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001365782.1:c.617C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_000366.6:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001018004.2:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001018005.2:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001018006.2:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001018007.2:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001018020.2:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001301244.2:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001365776.1:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001365777.1:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001365779.1:c.725C>T"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001365778.1:c.851C>T"}, {"type": "HGVS, genomic, LRG", "value": "LRG_387:g.24960C>T"}, {"type": "HGVS, genomic, RefSeqGene", "value": "NG_007557.1:g.24960C>T"}, {"type": "HGVS, genomic, top level", "value": "NC_000015.10:g.63062598C>T", "integer_value": 38}, {"type": "HGVS, genomic, top level, previous", "value": "NC_000015.9:g.63354797C>T", "integer_value": 37}, {"type": "HGVS, incomplete", "value": "c.725C>T"}, {"type": "HGVS, previous", "value": "NM_000366.5:c.725C>T"}, {"type": "HGVS, previous", "value": "NM_001018005.1:c.725C>T"}, {"type": "HGVS, protein"}, {"type": "HGVS, protein", "value": "LRG_387p1:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001018008.1:p.Ala206Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001288218.1:p.Ala206Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001317273.1:p.Ala206Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001317275.1:p.Ala206Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001317280.1:p.Ala206Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001352709.1:p.Ala206Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001352710.1:p.Ala206Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001352711.1:p.Ala206Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_000357.3:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001018004.1:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001018005.1:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001018006.1:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001018007.1:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001018020.1:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001288173.1:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001352705.1:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001352706.1:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001352708.1:p.Ala242Val"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001352707.1:p.Ala284Val"}, {"type": "Location", "value": "NM_000366.5:exon 8"}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_000366.6:c.725C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001018004.2:c.725C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001018005.2:c.725C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001018006.2:c.725C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001018007.2:c.725C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001018008.2:c.617C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001018020.2:c.725C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001301244.2:c.725C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001301289.2:c.617C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001330344.2:c.617C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001330346.2:c.617C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001330351.2:c.617C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001365776.1:c.725C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001365777.1:c.725C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001365778.1:c.851C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001365779.1:c.725C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001365780.1:c.617C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001365781.2:c.617C>T"}]}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_001365782.1:c.617C>T"}]}, {"type": "ProteinChange1LetterCode", "value": "A206V"}, {"type": "ProteinChange1LetterCode", "value": "A242V"}, {"type": "ProteinChange1LetterCode", "value": "A284V"}], "cytogenic_locations": ["15q22.2"], "sequence_locations": [{"assembly": "GRCh38", "chr": "15", "accession": "NC_000015.10", "start": 63062598, "stop": 63062598, "display_start": 63062598, "display_stop": 63062598, "variant_length": 1, "assembly_accession_version": "GCF_000001405.38", "assembly_status": "current", "position_vcf": 63062598, "reference_allele_vcf": "C", "alternate_allele_vcf": "T"}, {"assembly": "GRCh37", "chr": "15", "accession": "NC_000015.9", "start": 63354797, "stop": 63354797, "display_start": 63354797, "display_stop": 63354797, "variant_length": 1, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous", "position_vcf": 63354797, "reference_allele_vcf": "C", "alternate_allele_vcf": "T"}], "measure_relationship": [{"type": "within single gene", "names": [{"value": {"type": "Preferred", "value": "tropomyosin 1"}}], "symbols": [{"value": {"type": "Preferred", "value": "TPM1"}}], "sequence_locations": [{"assembly": "GRCh38", "chr": "15", "accession": "NC_000015.10", "start": 63042747, "stop": 63071915, "display_start": 63042747, "display_stop": 63071915, "strand": "+", "assembly_accession_version": "GCF_000001405.38", "assembly_status": "current"}, {"assembly": "GRCh37", "chr": "15", "accession": "NC_000015.9", "start": 63334837, "stop": 63364113, "display_start": 63334837, "display_stop": 63364113, "strand": "+", "variant_length": 29277, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous"}], "xrefs": [{"db": "Gene", "id": "7168"}, {"db": "OMIM", "id": "191010", "type": "MIM"}, {"db": "HGNC", "id": "HGNC:12010"}], "comments": [{"text": "This gene is cited in the ACMG recommendations of 2013 (PubMed 23788249) for reporting incidental findings in exons.", "type": "public", "datasource": "NCBI curation"}, {"text": "This gene is cited in the ACMG recommendations of 2016 (PubMed 27854360) for reporting incidental findings in exons.", "type": "public", "datasource": "NCBI curation"}, {"text": "This gene is cited in the ACMG recommendations of 2021 (SF v3.0; PubMed 34012068) for reporting secondary findings in clinical exome and genome sequencing.", "type": "public", "datasource": "ClinVar"}, {"text": "This gene is cited in the ACMG recommendations of 2022 (SF v3.1; PubMed 35802134) for reporting secondary findings in clinical exome and genome sequencing.", "type": "public", "datasource": "ClinVar"}]}], "xrefs": [{"db": "dbSNP", "id": "397516387", "type": "rs"}], "id": 52607}], "names": [{"value": {"type": "Preferred", "value": "NM_001018005.2(TPM1):c.725C>T (p.Ala242Val)"}}, {"value": {"type": "Preferred", "value": "NM_001018005.2(TPM1):c.725C>T (p.Ala242Val)"}}, {"value": {"type": "Preferred", "value": "NM_001018005.2(TPM1):c.725C>T (p.Ala242Val)"}}, {"value": {"type": "Preferred", "value": "NM_001018005.2(TPM1):c.725C>T (p.Ala242Val)"}}, {"value": {"type": "Preferred", "value": "NM_001018005.2(TPM1):c.725C>T (p.Ala242Val)"}}, {"value": {"type": "Preferred", "value": "NM_001018005.2(TPM1):c.725C>T (p.Ala242Val)"}}], "xrefs": [{"db": "ClinGen", "id": "CA018297"}], "id": 43437}, "traits": {"type": "Disease", "traits": [{"type": "Disease", "names": [{"value": {"type": "Preferred", "value": "not specified"}}, {"value": {"type": "Alternate", "value": "AllHighlyPenetrant"}}], "attributes": [{"value": {"type": "public definition", "value": "The term 'not specified' was created for use in ClinVar so that submitters can convey the concept that a variant is benign, likely benign, or of uncertain significance for an unspecified set of disorders. This usage was introduced in 2014 to replace AllHighlyPenetrant."}}], "xrefs": [{"db": "MedGen", "id": "CN169374"}]}], "id": 9590}, "date_created": "2013-05-03", "date_last_updated": "2023-12-09", "id": 108203}, "record_status": "current", "replaces": ["RCV000152121"], "title": "NM_001018005.2(TPM1):c.725C>T (p.Ala242Val) AND not specified", "clinvar_assertions": [{"id": 101209, "submission_id": {"local_key": "27728264|not specified", "submitter": "Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine", "submitted_assembly": "GRCh37", "submitter_date": "2021-05-27"}, "clinvar_accession": {"acc": "SCV000060009", "version": 7, "type": "SCV", "date_updated": "2021-05-29", "date_created": "2013-05-03", "org_id": "21766", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "replaced_list": [{"accession": "SCV000200808", "version": 1, "date_changed": "2015-02-23"}], "clinical_significance": [{"review_status": "flagged submission", "descriptions": ["uncertain significance"], "citations": [{"ids": [{"source": "PubMed", "value": "24691700"}]}], "comments": [{"text": "The p.Ala242Val variant in TPM1 has been identified in one individual with LVNC (Tian 2015 PMID: 24691700), one individual with DCM and segregated with disease in one family member, but was also present in one unaffected family member (LMM data). This variant has also been identified in 1 of 113742 European alleles in gnomAD. Computational predictors predict that the variant is damaging. The residue is entirely conserved and no species harbor the variant amino acid. In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM2, PP3"}], "date_last_evaluated": "2020-08-12"}], "external_ids": [{"db": "Laboratory for Molecular Medicine", "id": "27728264"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "LMM Criteria"}, "citations": [{"ids": [{"source": "PubMed", "value": "24033266"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "unknown", "family_data": {"num_families_with_variant": 1}}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 3}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NC_000015.9:g.63354797C>T"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "TPM1"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "not specified"}}]}]}, "comments": [{"text": "Notes: None", "type": "FlaggedComment", "datasource": "ClinGen"}, {"text": "Reason: Older claim that does not account for recent evidence", "type": "FlaggedComment", "datasource": "ClinGen"}]}]} -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000038988", "version": 6, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2013-05-03"}, "record_status": "current", "clinical_significance": {"review_status": "no classifications from unflagged records", "description": "other", "date_last_evaluated": "2022-11-10"}, "assertion": "variation to disease", "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "not provided"}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 2}}, {"attribute": {"type": "NumFamiliesWithVariant", "integer_value": 1}}]}], "measures": {"type": "Variant", "acc": "VCV000045764", "version": 12, "measures": [{"type": "single nucleotide variant", "names": [{"value": {"type": "Preferred", "value": "NM_016239.4(MYO15A):c.8090T>C (p.Val2697Ala)"}}], "canonical_spdi": "NC_000017.11:18154131:T:C", "attributes": [{"type": "HGVS, coding, RefSeq", "value": "NM_016239.4:c.8090T>C"}, {"type": "HGVS, genomic, RefSeqGene", "value": "NG_011634.2:g.50427T>C"}, {"type": "HGVS, genomic, top level", "value": "NC_000017.11:g.18154132T>C", "integer_value": 38}, {"type": "HGVS, genomic, top level, previous", "value": "NC_000017.10:g.18057446T>C", "integer_value": 37}, {"type": "HGVS, incomplete", "value": "c.8090T>C"}, {"type": "HGVS, previous", "value": "NM_016239.3:c.8090T>C"}, {"type": "HGVS, previous", "value": "NG_011634.1:g.50427T>C"}, {"type": "HGVS, protein, RefSeq", "value": "NP_057323.3:p.Val2697Ala"}, {"type": "Location", "value": "NM_016239.3:exon 44"}, {"type": "MolecularConsequence", "value": "missense variant", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001583"}, {"db": "RefSeq", "id": "NM_016239.4:c.8090T>C"}]}, {"type": "ProteinChange1LetterCode", "value": "V2697A"}], "cytogenic_locations": ["17p11.2"], "sequence_locations": [{"assembly": "GRCh38", "chr": "17", "accession": "NC_000017.11", "start": 18154132, "stop": 18154132, "display_start": 18154132, "display_stop": 18154132, "variant_length": 1, "assembly_accession_version": "GCF_000001405.38", "assembly_status": "current", "position_vcf": 18154132, "reference_allele_vcf": "T", "alternate_allele_vcf": "C"}, {"assembly": "GRCh37", "chr": "17", "accession": "NC_000017.10", "start": 18057446, "stop": 18057446, "display_start": 18057446, "display_stop": 18057446, "variant_length": 1, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous", "position_vcf": 18057446, "reference_allele_vcf": "T", "alternate_allele_vcf": "C"}], "measure_relationship": [{"type": "within single gene", "names": [{"value": {"type": "Preferred", "value": "myosin XVA"}}], "symbols": [{"value": {"type": "Preferred", "value": "MYO15A"}}], "sequence_locations": [{"assembly": "GRCh38", "chr": "17", "accession": "NC_000017.11", "start": 18108756, "stop": 18179800, "display_start": 18108756, "display_stop": 18179800, "strand": "+", "assembly_accession_version": "GCF_000001405.38", "assembly_status": "current"}, {"assembly": "GRCh37", "chr": "17", "accession": "NC_000017.10", "start": 18012019, "stop": 18083115, "display_start": 18012019, "display_stop": 18083115, "strand": "+", "variant_length": 71097, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous"}], "xrefs": [{"db": "Gene", "id": "51168"}, {"db": "OMIM", "id": "602666", "type": "MIM"}, {"db": "HGNC", "id": "HGNC:7594"}]}], "xrefs": [{"db": "dbSNP", "id": "200451098", "type": "rs"}], "id": 54929}], "names": [{"value": {"type": "Preferred", "value": "NM_016239.4(MYO15A):c.8090T>C (p.Val2697Ala)"}}, {"value": {"type": "Preferred", "value": "NM_016239.4(MYO15A):c.8090T>C (p.Val2697Ala)"}}, {"value": {"type": "Preferred", "value": "NM_016239.4(MYO15A):c.8090T>C (p.Val2697Ala)"}}], "attributes": [{"type": "SubmitterVariantId", "value": "GDX:742872"}], "xrefs": [{"db": "ClinGen", "id": "CA137016"}], "id": 45764}, "traits": {"type": "Disease", "traits": [{"type": "Disease", "names": [{"value": {"type": "Preferred", "value": "not specified"}}, {"value": {"type": "Alternate", "value": "AllHighlyPenetrant"}}], "attributes": [{"value": {"type": "public definition", "value": "The term 'not specified' was created for use in ClinVar so that submitters can convey the concept that a variant is benign, likely benign, or of uncertain significance for an unspecified set of disorders. This usage was introduced in 2014 to replace AllHighlyPenetrant."}}], "xrefs": [{"db": "MedGen", "id": "CN169374"}]}], "id": 9590}, "date_created": "2013-05-03", "date_last_updated": "2023-12-09", "id": 110836}, "record_status": "current", "title": "NM_016239.4(MYO15A):c.8090T>C (p.Val2697Ala) AND not specified", "clinvar_assertions": [{"id": 103866, "submission_id": {"local_key": "38035533|not specified", "submitter": "Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine", "submitted_assembly": "GRCh37", "submitter_date": "2019-03-21"}, "clinvar_accession": {"acc": "SCV000062666", "version": 6, "type": "SCV", "date_updated": "2015-01-31", "date_created": "2013-05-03", "org_id": "21766", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "flagged submission", "descriptions": ["uncertain significance"], "comments": [{"text": "Variant classified as Uncertain Significance - Favor Pathogenic. The Val2697Ala variant has not been reported in the literature, but has been previously identif ied in 1 proband with hearing loss in trans with another variant of unknown sign ificance in MYO15A and segregated in 2 affected relatives (LMM unpublished data) . This variant has been reported in dbSNP (rs200451098) with no validation or a llele frequency information. Computational analyses (biochemical amino acid pro perties, conservation, AlignGVGD, PolyPhen2, and SIFT) suggest that the Val2697A la variant may impact the protein, though this information is not predictive eno ugh to determine pathogenicity. In summary, the clinical significance of this va riant cannot be determined with certainty; however, based upon its co-occurrence in trans with another MYO15A varaint in inviduals with hearing loss and in sili co prediction, we lean towards a more likely pathogenic role."}], "date_last_evaluated": "2012-11-20"}], "external_ids": [{"db": "Laboratory for Molecular Medicine", "id": "38035533"}], "attributes": [{"attribute": {"type": "AssertionMethod", "value": "LMM Criteria"}, "citations": [{"ids": [{"source": "PubMed", "value": "24033266"}]}]}], "observed_in": [{"sample": {"origin": "germline", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "not provided", "family_data": {"num_families_with_variant": 1}}, "methods": ["clinical testing"], "observed_data": [{"attribute": {"type": "VariantAlleles", "integer_value": 2}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "names": [{"value": {"type": "Alternate", "value": "NM_016239.3:c.8090T>C"}}, {"value": {"type": "Alternate", "value": "p.Val2697Ala"}}], "attributes": [{"type": "Location", "value": "NM_016239.3:EXON 44"}, {"type": "HGVS", "value": "NC_000017.10:g.18057446T>C"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "MYO15A"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "not specified"}}]}]}, "comments": [{"text": "Notes: None", "type": "FlaggedComment", "datasource": "ClinGen"}, {"text": "Reason: Older claim that does not account for recent evidence", "type": "FlaggedComment", "datasource": "ClinGen"}]}]} -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000115042", "version": 3, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2014-05-09"}, "record_status": "current", "clinical_significance": {"review_status": "no classifications from unflagged records", "description": "other"}, "assertion": "variation to disease", "observed_in": [{"sample": {"origin": "germline", "ethnicity": "Arab", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["research"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "acc": "VCV000127244", "version": 1, "measures": [{"type": "single nucleotide variant", "names": [{"value": {"type": "Preferred", "value": "NM_014780.5(CUL7):c.2592T>G (p.Tyr864Ter)"}}], "canonical_spdi": "NC_000006.12:43046303:A:C", "attributes": [{"type": "FunctionalConsequence", "value": "protein loss of function", "xrefs": [{"db": "Variation Ontology", "id": "0043"}]}, {"type": "HGVS, coding, RefSeq", "value": "NM_001374873.1:c.2592T>G"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001374874.1:c.2592T>G"}, {"type": "HGVS, coding, RefSeq", "value": "NM_014780.5:c.2592T>G"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001168370.2:c.2688T>G"}, {"type": "HGVS, coding, RefSeq", "value": "NM_001374872.1:c.2688T>G"}, {"type": "HGVS, genomic, RefSeqGene", "value": "NG_016205.1:g.12642T>G"}, {"type": "HGVS, genomic, top level", "value": "NC_000006.12:g.43046304A>C", "integer_value": 38}, {"type": "HGVS, genomic, top level, previous", "value": "NC_000006.11:g.43014042A>C", "integer_value": 37}, {"type": "HGVS, previous", "value": "NM_001168370.1:c.2844T>G"}, {"type": "HGVS, protein", "value": "p.Y948*"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001361802.1:p.Tyr864Ter"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001361803.1:p.Tyr864Ter"}, {"type": "HGVS, protein, RefSeq", "value": "NP_055595.2:p.Tyr864Ter"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001161842.2:p.Tyr896Ter"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001361801.1:p.Tyr896Ter"}, {"type": "HGVS, protein, RefSeq", "value": "NP_001161842.1:p.Tyr948Ter"}, {"type": "MolecularConsequence", "value": "nonsense", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001587"}, {"db": "RefSeq", "id": "NM_001168370.2:c.2688T>G"}]}, {"type": "MolecularConsequence", "value": "nonsense", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001587"}, {"db": "RefSeq", "id": "NM_001374872.1:c.2688T>G"}]}, {"type": "MolecularConsequence", "value": "nonsense", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001587"}, {"db": "RefSeq", "id": "NM_001374873.1:c.2592T>G"}]}, {"type": "MolecularConsequence", "value": "nonsense", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001587"}, {"db": "RefSeq", "id": "NM_001374874.1:c.2592T>G"}]}, {"type": "MolecularConsequence", "value": "nonsense", "xrefs": [{"db": "Sequence Ontology", "id": "SO:0001587"}, {"db": "RefSeq", "id": "NM_014780.5:c.2592T>G"}]}, {"type": "ProteinChange1LetterCode", "value": "Y864*"}, {"type": "ProteinChange1LetterCode", "value": "Y896*"}, {"type": "ProteinChange1LetterCode", "value": "Y948*"}], "global_minor_allele_frequency": {"value": 0.0002, "source": "1000 Genomes Project", "minor_allele": "G"}, "cytogenic_locations": ["6p21.1"], "sequence_locations": [{"assembly": "GRCh38", "chr": "6", "accession": "NC_000006.12", "start": 43046304, "stop": 43046304, "display_start": 43046304, "display_stop": 43046304, "variant_length": 1, "assembly_accession_version": "GCF_000001405.38", "assembly_status": "current", "position_vcf": 43046304, "reference_allele_vcf": "A", "alternate_allele_vcf": "C"}, {"assembly": "GRCh37", "chr": "6", "accession": "NC_000006.11", "start": 43014042, "stop": 43014042, "display_start": 43014042, "display_stop": 43014042, "variant_length": 1, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous", "position_vcf": 43014042, "reference_allele_vcf": "A", "alternate_allele_vcf": "C"}], "measure_relationship": [{"type": "within single gene", "names": [{"value": {"type": "Preferred", "value": "cullin 7"}}], "symbols": [{"value": {"type": "Preferred", "value": "CUL7"}}], "sequence_locations": [{"assembly": "GRCh38", "chr": "6", "accession": "NC_000006.12", "start": 43037617, "stop": 43053851, "display_start": 43037617, "display_stop": 43053851, "strand": "-", "assembly_accession_version": "GCF_000001405.38", "assembly_status": "current"}, {"assembly": "GRCh37", "chr": "6", "accession": "NC_000006.11", "start": 43005354, "stop": 43021682, "display_start": 43005354, "display_stop": 43021682, "strand": "-", "variant_length": 16329, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous"}], "xrefs": [{"db": "Gene", "id": "9820"}, {"db": "OMIM", "id": "609577", "type": "MIM"}, {"db": "HGNC", "id": "HGNC:21024"}]}], "xrefs": [{"db": "dbSNP", "id": "201406974", "type": "rs"}], "id": 132701}], "names": [{"value": {"type": "Preferred", "value": "NM_014780.5(CUL7):c.2592T>G (p.Tyr864Ter)"}}, {"value": {"type": "Preferred", "value": "NM_014780.5(CUL7):c.2592T>G (p.Tyr864Ter)"}}], "xrefs": [{"db": "ClinGen", "id": "CA236446"}], "id": 127244}, "traits": {"type": "Disease", "traits": [{"type": "Disease", "names": [{"value": {"type": "Preferred", "value": "3M syndrome 1"}, "xrefs": [{"db": "MONDO", "id": "MONDO:0010117"}]}, {"value": {"type": "Alternate", "value": "Three M syndrome 1"}, "xrefs": [{"db": "Genetic Alliance", "id": "Three+M+syndrome/7072"}]}], "symbols": [{"value": {"type": "Alternate", "value": "3M1"}, "xrefs": [{"db": "OMIM", "id": "273750", "type": "MIM"}]}], "attributes": [{"value": {"type": "public definition", "value": "Three M syndrome is characterized by severe pre- and postnatal growth deficiency (final height 5-6 SD below the mean; i.e., 120-130 cm), characteristic facies, and normal intelligence. Additional features of three M syndrome include short broad neck, prominent trapezii, deformed sternum, short thorax, square shoulders, winged scapulae, hyperlordosis, short fifth fingers, prominent heels, and loose joints. Males with three M syndrome have hypogonadism and occasionally hypospadias."}, "xrefs": [{"db": "GeneReviews", "id": "NBK1481"}]}, {"value": {"type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "15239"}]}], "citations": [{"ids": [{"source": "PubMed", "value": "20301654"}, {"source": "BookShelf", "value": "NBK1481"}], "type": "review", "abbrev": "GeneReviews"}, {"ids": [{"source": "PubMed", "value": "21364696"}], "type": "Translational/Evidence-based", "abbrev": "EuroGentest, 2011"}], "xrefs": [{"db": "MONDO", "id": "MONDO:0010117"}, {"db": "MedGen", "id": "C2678312"}, {"db": "Orphanet", "id": "2616"}, {"db": "OMIM", "id": "273750", "type": "MIM"}]}], "id": 415}, "date_created": "2014-05-09", "date_last_updated": "2023-12-09", "id": 269569}, "record_status": "current", "title": "NM_014780.5(CUL7):c.2592T>G (p.Tyr864Ter) AND 3M syndrome 1", "clinvar_assertions": [{"id": 269551, "submission_id": {"local_key": "NM_001168370.1:c.2844T>G|OMIM:273750", "submitter": 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"NCBI"}, {"text": "Notes: SCV000108552 appears to be redundant with SCV000221722.", "type": "FlaggedComment", "datasource": "NCBI"}]}]} -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000115045", "version": 3, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2014-05-09"}, "record_status": "current", "clinical_significance": {"review_status": "no classifications from unflagged records", "description": "other"}, "assertion": "variation to disease", "observed_in": [{"sample": {"origin": "germline", "ethnicity": "Arab", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes"}, "methods": ["research"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "acc": "VCV000127247", "version": 1, "measures": [{"type": "single nucleotide variant", "names": [{"value": {"type": "Preferred", "value": "NM_006031.6(PCNT):c.196G>T (p.Gly66Ter)"}}], "canonical_spdi": 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"NM_006031.6(PCNT):c.196G>T (p.Gly66Ter)"}}, {"value": {"type": "Preferred", "value": "NM_006031.6(PCNT):c.196G>T (p.Gly66Ter)"}}], "xrefs": [{"db": "ClinGen", "id": "CA236167"}], "id": 127247}, "traits": {"type": "Disease", "traits": [{"type": "Disease", "names": [{"value": {"type": "Preferred", "value": "Microcephalic osteodysplastic primordial dwarfism type II"}, "xrefs": [{"db": "GeneTests", "id": "301116"}, {"db": "MONDO", "id": "MONDO:0008872"}]}, {"value": {"type": "Alternate", "value": "MOPD II"}, "xrefs": [{"db": "OMIM", "id": "210720", "type": "MIM"}]}, {"value": {"type": "Alternate", "value": "OSTEODYSPLASTIC PRIMORDIAL DWARFISM, TYPE II"}, "xrefs": [{"db": "OMIM", "id": "210720", "type": "MIM"}]}, {"value": {"type": "Alternate", "value": "Microcephalic osteodysplastic primordial dwarfism type 2"}, "xrefs": [{"db": "Genetic Alliance", "id": "Microcephalic+osteodysplastic+primordial+dwarfism+type+2/4731"}]}, {"value": {"type": "Alternate", "value": "MOPD 2"}}, {"value": 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Associated features that differentiate it from other forms of primordial dwarfism and that may necessitate treatment include: abnormal dentition, a slender bone skeletal dysplasia with hip deformity and/or scoliosis, insulin resistance / diabetes mellitus, chronic kidney disease, cardiac malformations, and global vascular disease. The latter includes neurovascular disease such as moyamoya vasculopathy and intracranial aneurysms (which can lead to strokes), coronary artery disease (which can lead to premature myocardial infarctions), and renal vascular disease. Hypertension, which is also common, can have multiple underlying causes given the complex comorbidities."}, "xrefs": [{"db": "GeneReviews", "id": "NBK575926"}]}, {"value": {"type": "GARD id"}, "xrefs": [{"db": "Office of Rare Diseases", "id": "9844"}]}], "citations": [{"ids": [{"source": "PubMed", "value": "34978779"}, {"source": "BookShelf", "value": "NBK575926"}], "type": "review", "abbrev": "GeneReviews"}], "xrefs": [{"db": "MONDO", "id": "MONDO:0008872"}, {"db": "MedGen", "id": "C0432246"}, {"db": "Orphanet", "id": "2637"}, {"db": "OMIM", "id": "210720", "type": "MIM"}]}], "id": 1291}, "date_created": "2014-05-09", "date_last_updated": "2023-12-09", "id": 269572}, "record_status": "current", "title": "NM_006031.6(PCNT):c.196G>T (p.Gly66Ter) AND Microcephalic osteodysplastic primordial dwarfism type II", "clinvar_assertions": [{"id": 269554, "submission_id": {"local_key": "NM_006031.5:c.196G>T|OMIM:210720", "submitter": "Developmental Genetics Unit, King Faisal Specialist Hospital & Research Centre", "submitter_date": "2014-05-08"}, "clinvar_accession": {"acc": "SCV000108550", "version": 1, "type": "SCV", "date_updated": "2014-05-09", "date_created": "2014-05-09", "org_id": "500184", "org_type": "primary", "org_category": "laboratory"}, "assertion_type": "variation to disease", "record_status": "current", "clinical_significance": [{"review_status": "flagged submission", "descriptions": ["pathogenic"]}], "observed_in": [{"sample": {"origin": "germline", "ethnicity": "Arab", "geographic_origin": "Saudi Arabia", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "yes", "gender": "male"}, "methods": ["research"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}], "traits": {"type": "Disease", "traits": [{"type": "Finding", "names": [{"value": {"type": "Preferred", "value": "Preterm, IUGR, delayed motor and speech development, high-pitched voice and recurrent chest infections"}}]}]}}], "measures": {"type": "Variant", "measures": [{"type": "variation", "names": [{"value": {"type": "Alternate", "value": "p.Gly66*"}}], "attributes": [{"type": "FunctionalConsequence", "value": "protein loss of function", "xrefs": [{"db": "Variation Ontology", "id": "0043", "url": "http://www.variationontology.org/cgi-bin/amivario/term-details.cgi?term=VariO:0043"}]}, {"type": "HGVS", "value": "NM_006031.5:c.196G>T"}], "measure_relationship": [{"type": "variant in gene", "symbols": [{"value": {"type": "Preferred", "value": "PCNT"}}]}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "Microcephalic osteodysplastic primordial dwarfism type 2"}}], "xrefs": [{"db": "OMIM", "id": "210720", "type": "MIM"}]}]}, "study_name": "Genomic Analysis of Primordial Dwarfism Reveals Novel Disease Genes", "comments": [{"text": "Reason: This record appears to be redundant with a more recent record from the same submitter.", "type": "FlaggedComment", "datasource": "NCBI"}, {"text": "Notes: SCV000108550 appears to be redundant with SCV000221549.", "type": "FlaggedComment", "datasource": "NCBI"}]}]} -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000124219", "version": 5, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2014-06-23"}, "record_status": "current", "clinical_significance": {"review_status": "no classifications from unflagged records", "description": "other"}, "assertion": "variation to disease", "observed_in": [{"sample": {"origin": "not provided", "species": {"value": "human", "taxonomy_id": 9606}, "affected_status": "not provided", "number_tested": 1}, "methods": ["literature only"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "acc": "VCV000136709", "version": 11, "measures": [{"type": "single nucleotide variant", "names": [{"value": {"type": "Preferred", "value": "NM_001323289.2(CDKL5):c.145+17A>G"}}], "canonical_spdi": "NC_000023.11:18564538:A:G", 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{"origin": "not provided", "species": {"value": "human"}, "affected_status": "not provided", "number_tested": 1}, "methods": ["not provided"], "observed_data": [{"attribute": {"type": "Description", "value": "not provided"}}]}], "measures": {"type": "Variant", "measures": [{"type": "variation", "attributes": [{"type": "HGVS", "value": "NM_003159.2:c.145+17A>G"}]}]}, "traits": {"type": "Disease", "traits": [{"names": [{"value": {"type": "Preferred", "value": "not provided"}}]}]}, "comments": [{"text": "Reason: This record appears to be redundant with a more recent record from the same submitter.", "type": "FlaggedComment", "datasource": "NCBI"}, {"text": "Notes: SCV000189197 appears to be redundant with SCV000222252.", "type": "FlaggedComment", "datasource": "NCBI"}]}]} -{"reference_clinvar_assertion": {"clinvar_accession": {"acc": "RCV000132997", "version": 3, "type": "RCV", "date_updated": "2023-12-09", "date_created": "2014-08-15"}, "record_status": "current", 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submitter", "sequence_location": {"assembly": "GRCh37", "chr": "13", "accession": "NC_000013.10", "outer_start": null, "inner_start": null, "start": 95248354, "stop": 95248354, "inner_stop": null, "outer_stop": null, "display_start": 95248354, "display_stop": 95248354, "strand": null, "variant_length": 1, "reference_allele": null, "alternate_allele": null, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous", "position_vcf": 95248354, "reference_allele_vcf": "G", "alternate_allele_vcf": "A", "for_display_length": null}, "hgnc_ids": ["HGNC:20324"], "absolute_copy_number": null, "reference_copy_number": null, "copy_number_tuple": null} -{"rcv": "RCV002510448", "variant_type": "single nucleotide variant", "clinical_significance": "likely pathogenic", "review_status": "criteria provided, single submitter", "sequence_location": {"assembly": "GRCh37", "chr": "13", "accession": "NC_000013.10", "outer_start": null, "inner_start": null, "start": 95243106, "stop": 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provided, multiple submitters, no conflicts", "sequence_location": {"assembly": "GRCh37", "chr": "13", "accession": "NC_000013.10", "outer_start": null, "inner_start": null, "start": 95243122, "stop": 95243122, "inner_stop": null, "outer_stop": null, "display_start": 95243122, "display_stop": 95243122, "strand": null, "variant_length": 1, "reference_allele": null, "alternate_allele": null, "assembly_accession_version": "GCF_000001405.25", "assembly_status": "previous", "position_vcf": 95243122, "reference_allele_vcf": "C", "alternate_allele_vcf": "A", "for_display_length": null}, "hgnc_ids": ["HGNC:20324"], "absolute_copy_number": null, "reference_copy_number": null, "copy_number_tuple": null} -{"rcv": "RCV000624586", "variant_type": "single nucleotide variant", "clinical_significance": "pathogenic", "review_status": "criteria provided, single submitter", "sequence_location": {"assembly": "GRCh37", "chr": "13", "accession": "NC_000013.10", "outer_start": null, "inner_start": null, 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+6,10 @@ set -x export TMPDIR=$(mktemp -d) trap "rm -rf $TMPDIR" EXIT -rm -rf tests/clinvar-sv/clinvar-sv-grch37.tsv.db +rm -rf tests/clinvar-sv/clinvar-sv-grch37.db cargo run --all-features -- \ clinvar-sv import -vvv \ --genome-release grch37 \ --path-in-jsonl tests/clinvar-sv/clinvar-variants-grch37-seqvars.jsonl \ --path-in-jsonl tests/clinvar-sv/clinvar-variants-grch37-strucvars.jsonl \ - --path-out-rocksdb tests/clinvar-sv/clinvar-sv-grch37.tsv.db + --path-out-rocksdb tests/clinvar-sv/clinvar-sv-grch37.db diff --git a/tests/clinvar-sv/clinvar-sv-grch37.db/000010.sst b/tests/clinvar-sv/clinvar-sv-grch37.db/000010.sst new file mode 100644 index 00000000..ed616da7 --- /dev/null +++ b/tests/clinvar-sv/clinvar-sv-grch37.db/000010.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c2ddad572e2fe4d88855c3e69e621e4d58a8a4023995bfdda82761fc4981771b +size 1363 diff --git a/tests/clinvar-sv/clinvar-sv-grch37.db/000012.sst 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