From 4626b8fd08b82b24d67aec10cd86b05ce9939337 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Fri, 6 Oct 2023 08:37:13 +0200 Subject: [PATCH] wip --- Cargo.lock | 4 +- README.md | 8 +- src/seqvars/ingest/mod.rs | 376 +++++++++++++----- ...sult_snapshot_test@NA12878_dragen_vcf.snap | 183 +++++++++ ...@example_dragen_07_021_624_3_10_4_vcf.snap | 56 +++ ...@example_dragen_07_021_624_3_10_9_vcf.snap | 56 +++ ...apshot_test@example_gatk_hc_3_7-0_vcf.snap | 60 +++ src/sv/query/schema.rs | 1 - 8 files changed, 646 insertions(+), 98 deletions(-) create mode 100644 src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap create mode 100644 src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap create mode 100644 src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap create mode 100644 src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap diff --git a/Cargo.lock b/Cargo.lock index 695c88fd..1853caba 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1789,9 +1789,9 @@ dependencies = [ [[package]] name = "mehari" -version = "0.9.0" +version = "0.10.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8734e86d72feb0568a9c0402e36eaa0625bf1b2d8da1a3f1c7ec03e02d0f5808" +checksum = "a95119609578b3515e0b3720c1a21a7a38cd2303a7557f5c0771372fc3d1fe4c" dependencies = [ "actix-web", "annonars", diff --git a/README.md b/README.md index f80d0da4..9f2a33a2 100644 --- a/README.md +++ b/README.md @@ -76,12 +76,12 @@ $ varfish-server-worker db mk-inhouse \ This command takes as the input a single VCF file from a (supported) variant caller and converts it into a file for further querying. The command interprets the following fields which are written out by the commonly used variant callers such as GATK UnifiedGenotyper, GATK HaplotypeCaller, and Illumina Dragen. -- `FORMAT/AD` -- allelic depth, one value per allele (including reference0) -- `FORMAT/DP` -- total read coverage -- `FORMAT/GQ` -- genotype quality - `FORMAT/GT` -- genotype +- `FORMAT/GQ` -- genotype quality +- `FORMAT/DP` -- total read coverage +- `FORMAT/AD` -- allelic depth, one value per allele (including reference0) - `FORMAT/PID` -- physical phasing information as written out by GATK HaplotypeCaller in GVCF workflow -- `FORMAT/PIS` -- physical phasing information as written out by Dragen variant caller +- `FORMAT/PS` -- physical phasing information as written out by Dragen variant caller - this field fill be written as `FORMAT/PID` - `FORMAT/SQ` -- "somatic quality" for each alternate allele, as written out by Illumina Dragen variant caller - this field will be written as `FORMAT/GQ` diff --git a/src/seqvars/ingest/mod.rs b/src/seqvars/ingest/mod.rs index 4853462b..133e1cac 100644 --- a/src/seqvars/ingest/mod.rs +++ b/src/seqvars/ingest/mod.rs @@ -1,6 +1,6 @@ //! Implementation of `seqvars ingest` subcommand. -use std::sync::Arc; +use std::sync::{Arc, OnceLock}; use crate::common::{self, GenomeRelease}; use mehari::annotate::seqvars::provider::MehariProvider; @@ -50,6 +50,173 @@ pub fn path_component(genomebuild: GenomeRelease) -> &'static str { } } +/// Known keys information and logic for `FORMAT`. +#[derive(Debug)] +struct KnownFormatKeys { + /// The keys that will be written to the output. + output_keys: Vec, + /// The keys that are known from the input keys. + known_keys: Vec, + /// Mapping from known to output keys where it is not identity + known_to_output_map: std::collections::HashMap< + vcf::record::genotypes::keys::Key, + vcf::record::genotypes::keys::Key, + >, +} + +impl Default for KnownFormatKeys { + /// Constructor. + fn default() -> Self { + Self { + output_keys: vec![ + vcf::record::genotypes::keys::key::GENOTYPE, // GT + vcf::record::genotypes::keys::key::CONDITIONAL_GENOTYPE_QUALITY, // GQ + vcf::record::genotypes::keys::key::READ_DEPTH, // DP + vcf::record::genotypes::keys::key::READ_DEPTHS, // AD + "PID".parse().expect("invalid key: PID"), + ], + known_keys: vec![ + vcf::record::genotypes::keys::key::GENOTYPE, + vcf::record::genotypes::keys::key::CONDITIONAL_GENOTYPE_QUALITY, + vcf::record::genotypes::keys::key::READ_DEPTH, + vcf::record::genotypes::keys::key::READ_DEPTHS, + "PID".parse().expect("invalid key: PID"), + "PS".parse().expect("invalid key: PS"), // written as PID + "SQ".parse().expect("invalid key: SQ"), // written as AD + ], + known_to_output_map: vec![ + ( + "PS".parse().expect("invalid key: PS"), + "PID".parse().expect("invalid key: PID"), + ), + ( + "SQ".parse().expect("invalid key: SQ"), + vcf::record::genotypes::keys::key::CONDITIONAL_GENOTYPE_QUALITY, + ), + ] + .into_iter() + .collect(), + } + } +} + +impl KnownFormatKeys { + /// Map from known to output key. + pub fn known_to_output( + &self, + key: &vcf::record::genotypes::keys::Key, + ) -> vcf::record::genotypes::keys::Key { + self.known_to_output_map.get(key).unwrap_or(key).clone() + } +} + +/// The known `FORMAT` keys. +static KNOWN_FORMAT_KEYS: OnceLock = OnceLock::new(); + +/// Transform the ``FORMAT`` key if known. +fn transform_format_value( + value: &Option<&vcf::record::genotypes::sample::Value>, + key: &vcf::record::genotypes::keys::Key, + allele_no: usize, +) -> Option> { + if let Some(value) = value { + Some(Some(match key.as_ref() { + "AD" => { + // Only write out current allele as AD. + match *value { + vcf::record::genotypes::sample::Value::Array( + vcf::record::genotypes::sample::value::Array::Integer(ad_values), + ) => vcf::record::genotypes::sample::Value::Integer( + ad_values[allele_no].expect("SQ should be integer value"), + ), + _ => return None, // unreachable!("FORMAT/AD must be array of integer"), + } + } + "PS" => { + // PS is written as PID. + match *value { + vcf::record::genotypes::sample::Value::Integer(ps_value) => { + vcf::record::genotypes::sample::Value::String(format!("{}", ps_value)) + } + _ => return None, // unreachable!("FORMAT/PS must be integer"), + } + } + "SQ" => { + // SQ is written as AD. + match *value { + vcf::record::genotypes::sample::Value::Float(sq_value) => { + vcf::record::genotypes::sample::Value::Float(*sq_value) + } + vcf::record::genotypes::sample::Value::Array( + vcf::record::genotypes::sample::value::Array::Float(sq_values), + ) => vcf::record::genotypes::sample::Value::Float( + sq_values[allele_no].expect("SQ should be float value"), + ), + _ => return None, // unreachable!("FORMAT/PS must be integer"), + } + } + _ => return None, // unreachable!("unknown key: {:?}", key), + })) + } else { + Some(None) + } +} + +/// Copy the `FORMAT/GQ` fields for all samples. +/// +/// The implementation assumes that there are no duplicates in the output keys when mapped +/// from input keys. +fn copy_format( + input_record: &vcf::Record, + builder: vcf::record::Builder, + idx_output_to_input: &[usize], + allele_no: usize, + known_format_keys: &KnownFormatKeys, +) -> Result { + let keys_from_input_known = input_record + .genotypes() + .keys() + .iter() + .filter(|k| known_format_keys.known_keys.contains(*k)) + .cloned() + .collect::>(); + let output_keys = keys_from_input_known + .iter() + .map(|k| known_format_keys.known_to_output(k).clone()) + .collect::>(); + + let values = idx_output_to_input + .iter() + .copied() + .map(|input_idx| { + let sample = input_record + .genotypes() + .get_index(input_idx) + .expect("input_idx must be valid here"); + keys_from_input_known + .iter() + .map(|key| { + let input_value = sample.get(key).expect("key must be valid"); + if let Some(value) = transform_format_value(&input_value, key, allele_no) { + value + } else if known_format_keys.output_keys.contains(key) { + input_value.map(|s| s.clone()) + } else { + unreachable!("don't know how to handle key: {:?}", key) + } + }) + .collect::>() + }) + .collect::>(); + + let genotypes = vcf::record::Genotypes::new( + vcf::record::genotypes::Keys::try_from(output_keys).expect("invalid keys"), + values, + ); + + Ok(builder.set_genotypes(genotypes)) +} + /// Process the variants from `input_reader` to `output_writer`. fn process_variants( output_writer: &mut vcf::Writer>, @@ -109,118 +276,145 @@ fn process_variants( let predictor = mehari::annotate::seqvars::csq::ConsequencePredictor::new(provider, assembly); tracing::info!("... done building transcript interval trees"); + // Build mapping from output sample index to input sample index. + let idx_output_to_input = { + let output_sample_to_idx = output_header + .sample_names() + .iter() + .enumerate() + .map(|(idx, name)| (name, idx)) + .collect::>(); + let mut res = vec![usize::MAX; output_header.sample_names().len()]; + for (input_idx, sample) in input_header.sample_names().iter().enumerate() { + res[output_sample_to_idx[sample]] = input_idx; + } + res + }; + // Read through input file, construct output records, and annotate these. let start = std::time::Instant::now(); let mut prev = std::time::Instant::now(); let mut total_written = 0usize; let mut records = input_reader.records(&input_header); + let known_format_keys = KNOWN_FORMAT_KEYS.get_or_init(Default::default); loop { if let Some(input_record) = records.next() { - let mut input_record = input_record?; - - for alt_allele in input_record.alternate_bases().iter() { - vcf::Record::builder() - .set_chromosome(input_record.chromosome().clone()) - .set_position(input_record.position()) - .set_reference_bases(input_record.reference_bases().clone()) - .set_alternate_bases(vcf::record::AlternateBases::from(vec![alt_allele.clone()])) - .build()?; - // FORMAT info missing - todo!(); - } - + let input_record = input_record?; + + for (allele_no, alt_allele) in input_record.alternate_bases().iter().enumerate() { + // Construct record with first few fields describing one variant allele. + let builder = vcf::Record::builder() + .set_chromosome(input_record.chromosome().clone()) + .set_position(input_record.position()) + .set_reference_bases(input_record.reference_bases().clone()) + .set_alternate_bases(vcf::record::AlternateBases::from(vec![ + alt_allele.clone() + ])); + + // Copy over the well-known FORMAT fields and construct output record. + let builder = copy_format( + &input_record, + builder, + &idx_output_to_input, + allele_no, + known_format_keys, + )?; - // TODO: ignores all but the first alternative allele! - let vcf_var = annonars::common::keys::Var::from_vcf_allele(&input_record, 0); + let mut output_record = builder.build()?; - // Skip records with a deletion as alternative allele. - if vcf_var.alternative == "*" { - continue; - } + // Obtain annonars variant key from current allele for RocksDB lookup. + let vcf_var = + annonars::common::keys::Var::from_vcf_allele(&output_record, allele_no); - if prev.elapsed().as_secs() >= 60 { - tracing::info!("at {:?}", &vcf_var); - prev = std::time::Instant::now(); - } + // Skip records with a deletion as alternative allele. + if vcf_var.alternative == "*" { + continue; + } - // Only attempt lookups into RocksDB for canonical contigs. - if annonars::common::cli::is_canonical(vcf_var.chrom.as_str()) { - // Build key for RocksDB database from `vcf_var`. - let key: Vec = vcf_var.clone().into(); + if prev.elapsed().as_secs() >= 60 { + tracing::info!("at {:?}", &vcf_var); + prev = std::time::Instant::now(); + } - // Annotate with frequency. - if mehari::annotate::seqvars::CHROM_AUTO.contains(vcf_var.chrom.as_str()) { - mehari::annotate::seqvars::annotate_record_auto( - &db_freq, - &cf_autosomal, - &key, - &mut input_record, - )?; - } else if mehari::annotate::seqvars::CHROM_XY.contains(vcf_var.chrom.as_str()) { - mehari::annotate::seqvars::annotate_record_xy( - &db_freq, - &cf_gonosomal, - &key, - &mut input_record, - )?; - } else if mehari::annotate::seqvars::CHROM_MT.contains(vcf_var.chrom.as_str()) { - mehari::annotate::seqvars::annotate_record_mt( - &db_freq, - &cf_mtdna, + // Only attempt lookups into RocksDB for canonical contigs. + if annonars::common::cli::is_canonical(vcf_var.chrom.as_str()) { + // Build key for RocksDB database from `vcf_var`. + let key: Vec = vcf_var.clone().into(); + + // Annotate with frequency. + if mehari::annotate::seqvars::CHROM_AUTO.contains(vcf_var.chrom.as_str()) { + mehari::annotate::seqvars::annotate_record_auto( + &db_freq, + &cf_autosomal, + &key, + &mut output_record, + )?; + } else if mehari::annotate::seqvars::CHROM_XY.contains(vcf_var.chrom.as_str()) { + mehari::annotate::seqvars::annotate_record_xy( + &db_freq, + &cf_gonosomal, + &key, + &mut output_record, + )?; + } else if mehari::annotate::seqvars::CHROM_MT.contains(vcf_var.chrom.as_str()) { + mehari::annotate::seqvars::annotate_record_mt( + &db_freq, + &cf_mtdna, + &key, + &mut output_record, + )?; + } else { + tracing::trace!( + "Record @{:?} on non-canonical chromosome, skipping.", + &vcf_var + ); + } + + // Annotate with ClinVar information. + mehari::annotate::seqvars::annotate_record_clinvar( + &db_clinvar, + &cf_clinvar, &key, - &mut input_record, + &mut output_record, )?; - } else { - tracing::trace!( - "Record @{:?} on non-canonical chromosome, skipping.", - &vcf_var - ); } - // Annotate with ClinVar information. - mehari::annotate::seqvars::annotate_record_clinvar( - &db_clinvar, - &cf_clinvar, - &key, - &mut input_record, - )?; - } - - let annonars::common::keys::Var { - chrom, - pos, - reference, - alternative, - } = vcf_var; - - // Annotate with variant effect. - if let Some(ann_fields) = - predictor.predict(&mehari::annotate::seqvars::csq::VcfVariant { - chromosome: chrom, - position: pos, + let annonars::common::keys::Var { + chrom, + pos, reference, alternative, - })? - { - if !ann_fields.is_empty() { - input_record.info_mut().insert( - "ANN".parse()?, - Some(vcf::record::info::field::Value::Array( - vcf::record::info::field::value::Array::String( - ann_fields.iter().map(|ann| Some(ann.to_string())).collect(), - ), - )), - ); + } = vcf_var; + + // Annotate with variant effect. + if let Some(ann_fields) = + predictor.predict(&mehari::annotate::seqvars::csq::VcfVariant { + chromosome: chrom, + position: pos, + reference, + alternative, + })? + { + if !ann_fields.is_empty() { + output_record.info_mut().insert( + "ANN".parse()?, + Some(vcf::record::info::field::Value::Array( + vcf::record::info::field::value::Array::String( + ann_fields.iter().map(|ann| Some(ann.to_string())).collect(), + ), + )), + ); + } } - } - // Write out the record. - output_writer.write_record(&output_header, &input_record)?; + // Write out the record. + output_writer.write_record(&output_header, &output_record)?; + total_written += 1; + } } else { break; // all done } - total_written += 1; if let Some(max_var_count) = args.max_var_count { if total_written >= max_var_count { tracing::warn!( @@ -327,14 +521,14 @@ mod test { #[case("tests/seqvars/ingest/NA12878_dragen.vcf")] #[case("tests/seqvars/ingest/Case_1.vcf")] fn result_snapshot_test(#[case] path: &str) -> Result<(), anyhow::Error> { - set_snapshot_suffix!("{:?}", path.split('/').last().unwrap().replace('.', "_")); + set_snapshot_suffix!("{}", path.split('/').last().unwrap().replace('.', "_")); let tmpdir = temp_testdir::TempDir::default(); let args_common = Default::default(); let args = super::Args { max_var_count: None, - path_mehari_db: Default::default(), + path_mehari_db: "tests/seqvars/ingest/db".into(), path_ped: path.replace(".vcf", ".ped"), genomebuild: GenomeRelease::Grch37, path_in: path.into(), diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap new file mode 100644 index 00000000..dff16473 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap @@ -0,0 +1,183 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +17 41244000 . T C . . gnomad_exomes_an=31346;gnomad_exomes_hom=1591;gnomad_exomes_het=6707;gnomad_genomes_an=250954;gnomad_genomes_hom=16402;gnomad_genomes_het=55703;clinvar_clinsig=benign;clinvar_rcv=RCV002490466;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.3548A>G|p.K1183R|3661/7088|3548/5592|1183/1864|2878|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.3407A>G|p.K1136R|3601/7028|3407/5451|1136/1817|2878|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-951A>G|p.?|895/3696|788/2100||-950|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3548A>G|p.K1183R|3661/7151|3548/5655|1183/1885|2878| GT:AD:DP:GQ 0/1:8:26:43 +17 41244435 . T C . . gnomad_exomes_an=31332;gnomad_exomes_hom=1505;gnomad_exomes_het=6415;gnomad_genomes_an=251032;gnomad_genomes_hom=16145;gnomad_genomes_het=55137;clinvar_clinsig=benign;clinvar_rcv=RCV001269365;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.3113A>G|p.E1038G|3226/7088|3113/5592|1038/1864|2443|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2972A>G|p.E991G|3166/7028|2972/5451|991/1817|2443|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-1386A>G|p.?|895/3696|788/2100||-1385|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3113A>G|p.E1038G|3226/7151|3113/5655|1038/1885|2443| GT:AD:DP:GQ 0/1:12:26:47 +17 41244936 . G A . . gnomad_exomes_an=31324;gnomad_exomes_hom=4287;gnomad_exomes_het=6594;gnomad_genomes_an=251034;gnomad_genomes_hom=22738;gnomad_genomes_het=55898;clinvar_clinsig=benign;clinvar_rcv=RCV002496522;ANN=A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2612C>T|p.P871L|2725/7088|2612/5592|871/1864|1942|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2471C>T|p.P824L|2665/7028|2471/5451|824/1817|1942|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1825C>T|p.?|894/3696|787/2100||1824|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2612C>T|p.P871L|2725/7151|2612/5655|871/1885|1942| GT:AD:DP:GQ 0/1:17:30:47 +17 41245237 . A G . . gnomad_exomes_an=31314;gnomad_exomes_hom=1492;gnomad_exomes_het=6416;gnomad_genomes_an=250946;gnomad_genomes_hom=16057;gnomad_genomes_het=55063;clinvar_clinsig=benign;clinvar_rcv=RCV000755639;ANN=G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2311T>C|p.L771=|2424/7088|2311/5592|771/1864|-1786|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2170T>C|p.L724=|2364/7028|2170/5451|724/1817|-1786|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1524T>C|p.?|894/3696|787/2100||1523|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2311T>C|p.L771=|2424/7151|2311/5655|771/1885|-1786| GT:AD:DP:GQ 0/1:18:29:46 +17 41245466 . G A . . gnomad_exomes_an=31338;gnomad_exomes_hom=1602;gnomad_exomes_het=6709;gnomad_genomes_an=251110;gnomad_genomes_hom=16420;gnomad_genomes_het=55707;clinvar_clinsig=benign;clinvar_rcv=RCV002477262;ANN=A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2082C>T|p.S694=|2195/7088|2082/5592|694/1864|-2015|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.1941C>T|p.S647=|2135/7028|1941/5451|647/1817|-2015|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1295C>T|p.?|894/3696|787/2100||1294|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2082C>T|p.S694=|2195/7151|2082/5655|694/1885|-2015| GT:AD:DP:GQ 0/1:11:19:48 +17 41247122 . A ACCT . . gnomad_exomes_an=31242;gnomad_exomes_hom=1750;gnomad_exomes_het=7017;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001709486;ANN=ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|9/22|c.671-246_671-245insAGG|p.?|784/7088|671/5592||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.530-246_530-245insAGG|p.?|724/7028|530/5451||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.671-246_671-245insAGG|p.?|778/3696|671/2100||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.671-246_671-245insAGG|p.?|784/7151|671/5655||-245| GT:AD:DP:GQ 0/1:18:29:45 +17 41247604 . A C . . gnomad_exomes_an=30832;gnomad_exomes_hom=1544;gnomad_exomes_het=6574;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001636715;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|9/22|c.670+259T>G|p.?|783/7088|670/5592||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.529+259T>G|p.?|723/7028|529/5451||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.670+259T>G|p.?|777/3696|670/2100||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.670+259T>G|p.?|783/7151|670/5655||258| GT:AD:DP:GQ 0/1:12:23:47 +17 41248164 . C T . . gnomad_exomes_an=31116;gnomad_exomes_hom=1468;gnomad_exomes_het=6372;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001668352;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-225G>A|p.?|707/7088|594/5592||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-225G>A|p.?|647/7028|453/5451||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-225G>A|p.?|701/3696|594/2100||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-225G>A|p.?|707/7151|594/5655||-224| GT:AD:DP:GQ 0/1:14:21:44 +17 41248393 . C CAAAAAAAAAA . . ANN=CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-455_594-454insTTTTTTTTTT|p.?|707/7088|594/5592||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-455_453-454insTTTTTTTTTT|p.?|647/7028|453/5451||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-455_594-454insTTTTTTTTTT|p.?|701/3696|594/2100||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-455_594-454insTTTTTTTTTT|p.?|707/7151|594/5655||-454| GT:AD:DP:GQ 0/1:9:16:48 +17 41248484 . G C . . gnomad_exomes_an=30426;gnomad_exomes_hom=1385;gnomad_exomes_het=6148;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001657973;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-545C>G|p.?|707/7088|594/5592||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-545C>G|p.?|647/7028|453/5451||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-545C>G|p.?|701/3696|594/2100||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-545C>G|p.?|707/7151|594/5655||-544| GT:AD:DP:GQ 0/1:11:20:48 +17 41248588 . CA C . . gnomad_exomes_an=12806;gnomad_exomes_hom=585;gnomad_exomes_het=4704;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-650delT|p.?|707/7088|594/5592||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-650delT|p.?|647/7028|453/5451||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-650delT|p.?|701/3696|594/2100||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-650delT|p.?|707/7151|594/5655||-649| GT:AD:DP:GQ 0/1:9:19:42 +17 41249094 . A G . . gnomad_exomes_an=31332;gnomad_exomes_hom=1602;gnomad_exomes_het=6703;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001610505;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.593+167T>C|p.?|706/7088|593/5592||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.452+167T>C|p.?|646/7028|452/5451||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.593+167T>C|p.?|700/3696|593/2100||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.593+167T>C|p.?|706/7151|593/5655||166| GT:AD:DP:GQ 0/1:9:16:48 +17 41249363 . TA T . . gnomad_exomes_an=31286;gnomad_exomes_hom=1497;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.548-58delT|p.?|661/7088|548/5592||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-58delT|p.?|601/7028|407/5451||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-58delT|p.?|655/3696|548/2100||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-58delT|p.?|661/7151|548/5655||-57| GT:AD:DP:GQ 0/1:12:25:48 +17 41250047 . C CT . . gnomad_exomes_an=22188;gnomad_exomes_hom=992;gnomad_exomes_het=4281;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.548-742_548-741insA|p.?|661/7088|548/5592||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-742_407-741insA|p.?|601/7028|407/5451||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-742_548-741insA|p.?|655/3696|548/2100||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-742_548-741insA|p.?|661/7151|548/5655||-741| GT:AD:DP:GQ 0/1:13:20:18 +17 41250678 . C CT . . gnomad_exomes_an=31058;gnomad_exomes_hom=1566;gnomad_exomes_het=6658;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191403;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+1113_547+1114insA|p.?|660/7088|547/5592||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+1113_406+1114insA|p.?|600/7028|406/5451||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+1113_547+1114insA|p.?|654/3696|547/2100||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+1113_547+1114insA|p.?|660/7151|547/5655||1113| GT:AD:DP:GQ 0/1:6:22:42 +17 41250923 . T C . . gnomad_exomes_an=29782;gnomad_exomes_hom=4187;gnomad_exomes_het=6234;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191405;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+869A>G|p.?|660/7088|547/5592||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+869A>G|p.?|600/7028|406/5451||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+869A>G|p.?|654/3696|547/2100||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+869A>G|p.?|660/7151|547/5655||868| GT:AD:DP:GQ 0/1:13:22:47 +17 41251495 . C G . . gnomad_exomes_an=30850;gnomad_exomes_hom=1491;gnomad_exomes_het=6363;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001640278;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+297G>C|p.?|660/7088|547/5592||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+297G>C|p.?|600/7028|406/5451||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+297G>C|p.?|654/3696|547/2100||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+297G>C|p.?|660/7151|547/5655||296| GT:AD:DP:GQ 0/1:11:26:48 +17 41251646 . T A . . gnomad_exomes_an=31294;gnomad_exomes_hom=1592;gnomad_exomes_het=6693;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV002345409;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+146A>T|p.?|660/7088|547/5592||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+146A>T|p.?|600/7028|406/5451||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+146A>T|p.?|654/3696|547/2100||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+146A>T|p.?|660/7151|547/5655||145| GT:AD:DP:GQ 0/1:11:19:48 +17 41252575 . G A . . gnomad_exomes_an=6888;gnomad_exomes_hom=193;gnomad_exomes_het=1277;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191411;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-678C>T|p.?|555/7088|442/5592||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-678C>T|p.?|495/7028|301/5451||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-678C>T|p.?|549/3696|442/2100||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-678C>T|p.?|555/7151|442/5655||-677| GT:AD:DP:GQ:PID 1|1:0:3:5:41252575 +17 41252591 . C CAT . . gnomad_exomes_an=10332;gnomad_exomes_hom=95;gnomad_exomes_het=571;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-695_442-694insAT|p.?|555/7088|442/5592||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-695_301-694insAT|p.?|495/7028|301/5451||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-695_442-694insAT|p.?|549/3696|442/2100||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-695_442-694insAT|p.?|555/7151|442/5655||-694| GT:AD:DP:GQ:PID 1|1:0:2:4:41252575 +17 41254174 . A G . . gnomad_exomes_an=30142;gnomad_exomes_hom=1576;gnomad_exomes_het=6550;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191423;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1965T>C|p.?|554/7088|441/5592||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1965T>C|p.?|494/7028|300/5451||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1965T>C|p.?|548/3696|441/2100||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1965T>C|p.?|554/7151|441/5655||1964| GT:AD:DP:GQ 0/1:14:27:48 +17 41254374 . C CTTTTTTTT . . gnomad_exomes_an=15994;gnomad_exomes_hom=494;gnomad_exomes_het=1743;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1764_441+1765insAAAAAAAA|p.?|554/7088|441/5592||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1764_300+1765insAAAAAAAA|p.?|494/7028|300/5451||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1764_441+1765insAAAAAAAA|p.?|548/3696|441/2100||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1764_441+1765insAAAAAAAA|p.?|554/7151|441/5655||1764| GT:AD:DP:GQ 0/1:6:13:48 +17 41254405 . C T . . gnomad_exomes_an=24316;gnomad_exomes_hom=1000;gnomad_exomes_het=4795;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256092;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1734G>A|p.?|554/7088|441/5592||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1734G>A|p.?|494/7028|300/5451||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1734G>A|p.?|548/3696|441/2100||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1734G>A|p.?|554/7151|441/5655||1733| GT:AD:DP:GQ 0/1:5:14:43 +17 41254486 . T G . . gnomad_exomes_an=30560;gnomad_exomes_hom=4284;gnomad_exomes_het=6345;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191424;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1653A>C|p.?|554/7088|441/5592||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1653A>C|p.?|494/7028|300/5451||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1653A>C|p.?|548/3696|441/2100||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1653A>C|p.?|554/7151|441/5655||1652| GT:AD:DP:GQ 0/1:8:23:46 +17 41254965 . C CT . . gnomad_exomes_an=26726;gnomad_exomes_hom=2359;gnomad_exomes_het=6380;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255713;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1173_441+1174insA|p.?|554/7088|441/5592||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1173_300+1174insA|p.?|494/7028|300/5451||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1173_441+1174insA|p.?|548/3696|441/2100||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1173_441+1174insA|p.?|554/7151|441/5655||1173| GT:AD:DP:GQ 0/1:14:22:22 +17 41255102 . A G . . gnomad_exomes_an=31104;gnomad_exomes_hom=1426;gnomad_exomes_het=6400;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191428;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1037T>C|p.?|554/7088|441/5592||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1037T>C|p.?|494/7028|300/5451||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1037T>C|p.?|548/3696|441/2100||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1037T>C|p.?|554/7151|441/5655||1036| GT:AD:DP:GQ:PID 0|1:19:31:46:41255102 +17 41255111 . A T . . gnomad_exomes_an=31114;gnomad_exomes_hom=1530;gnomad_exomes_het=6684;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191429;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1028T>A|p.?|554/7088|441/5592||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1028T>A|p.?|494/7028|300/5451||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1028T>A|p.?|548/3696|441/2100||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1028T>A|p.?|554/7151|441/5655||1027| GT:AD:DP:GQ:PID 0|1:19:31:46:41255102 +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PID 0|1:11:17:43:41256074 +17 41256089 . AAAAAAAAAGAAAAG A . . gnomad_exomes_an=28388;gnomad_exomes_hom=1079;gnomad_exomes_het=5744;gnomad_genomes_an=167932;gnomad_genomes_hom=9911;gnomad_genomes_het=23697;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7088|441/5592||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+36_300+49delCTTTTCTTTTTTTT|p.?|494/7028|300/5451||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|548/3696|441/2100||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7151|441/5655||35| GT:AD:DP:GQ:PID 0|1:13:19:43:41256074 +17 41257134 . T C . . gnomad_exomes_an=31346;gnomad_exomes_hom=4418;gnomad_exomes_het=6505;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV002415590;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.213-161A>G|p.?|326/7088|213/5592||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-161A>G|p.?|266/7028|72/5451||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-161A>G|p.?|320/3696|213/2100||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-161A>G|p.?|326/7151|213/5655||-160| GT:AD:DP:GQ 0/1:14:29:48 +17 41257458 . A C . . gnomad_exomes_an=31258;gnomad_exomes_hom=1500;gnomad_exomes_het=6414;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191434;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.213-485T>G|p.?|326/7088|213/5592||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-485T>G|p.?|266/7028|72/5451||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-485T>G|p.?|320/3696|213/2100||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-485T>G|p.?|326/7151|213/5655||-484| GT:AD:DP:GQ 0/1:11:26:48 +17 41258043 . C T . . gnomad_exomes_an=30426;gnomad_exomes_hom=1538;gnomad_exomes_het=6460;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191436;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.212+430G>A|p.?|325/7088|212/5592||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+430G>A|p.?|265/7028|71/5451||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+430G>A|p.?|319/3696|212/2100||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+430G>A|p.?|325/7151|212/5655||429| GT:AD:DP:GQ 0/1:14:27:48 +17 41258135 . T TA . . gnomad_exomes_an=20132;gnomad_exomes_hom=1;gnomad_exomes_het=267;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.212+337_212+338insT|p.?|325/7088|212/5592||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+337_71+338insT|p.?|265/7028|71/5451||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+337_212+338insT|p.?|319/3696|212/2100||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+337_212+338insT|p.?|325/7151|212/5655||337| GT:AD:DP:GQ 1/1:3:14:4 +17 41259049 . C T . . gnomad_exomes_an=30790;gnomad_exomes_hom=1585;gnomad_exomes_het=6633;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191440;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-499G>A|p.?|248/7088|135/5592||-498|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-499G>A|p.?|188/7028|-7/5451||-498|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-499G>A|p.?|242/3696|135/2100||-498|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-499G>A|p.?|248/7151|135/5655||-498| GT:AD:DP:GQ 0/1:8:16:48 +17 41259079 . A ATT . . gnomad_exomes_an=21472;gnomad_exomes_hom=898;gnomad_exomes_het=3635;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-530_135-529insAA|p.?|248/7088|135/5592||-529|,ATT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-530_-7-529insAA|p.?|188/7028|-7/5451||-529|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-530_135-529insAA|p.?|242/3696|135/2100||-529|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-530_135-529insAA|p.?|248/7151|135/5655||-529| GT:AD:DP:GQ 0/1:10:13:7 +17 41259113 . G A . . gnomad_exomes_an=26218;gnomad_exomes_hom=2;gnomad_exomes_het=204;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255936;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-563C>T|p.?|248/7088|135/5592||-562|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-563C>T|p.?|188/7028|-7/5451||-562|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-563C>T|p.?|242/3696|135/2100||-562|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-563C>T|p.?|248/7151|135/5655||-562| GT:AD:DP:GQ 0/1:11:19:48 +17 41260352 . C CA . . gnomad_exomes_an=19754;gnomad_exomes_hom=856;gnomad_exomes_het=4728;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255985;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-1803_135-1802insT|p.?|248/7088|135/5592||-1802|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-1803_-7-1802insT|p.?|188/7028|-7/5451||-1802|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-1803_135-1802insT|p.?|242/3696|135/2100||-1802|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-1803_135-1802insT|p.?|248/7151|135/5655||-1802| GT:AD:DP:GQ 0/1:11:19:43 +17 41260723 . C CAAAAA . . ANN=CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2174_135-2173insTTTTT|p.?|248/7088|135/5592||-2173|,CAAAAA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2174_-7-2173insTTTTT|p.?|188/7028|-7/5451||-2173|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2174_135-2173insTTTTT|p.?|242/3696|135/2100||-2173|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2174_135-2173insTTTTT|p.?|248/7151|135/5655||-2173| GT:AD:DP:GQ 0/1:1:2:20 +17 41260808 . A G . . gnomad_exomes_an=30782;gnomad_exomes_hom=1558;gnomad_exomes_het=6565;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191445;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2258T>C|p.?|248/7088|135/5592||-2257|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2258T>C|p.?|188/7028|-7/5451||-2257|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2258T>C|p.?|242/3696|135/2100||-2257|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2258T>C|p.?|248/7151|135/5655||-2257| GT:AD:DP:GQ 0/1:12:15:32 +17 41261058 . T TCTATCTATCTACCTAC . . gnomad_exomes_an=31232;gnomad_exomes_hom=1461;gnomad_exomes_het=6772;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255302;ANN=TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7088|135/5592||-2508|,TCTATCTATCTACCTAC|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2509_-7-2508insGTAGGTAGATAGATAG|p.?|188/7028|-7/5451||-2508|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|242/3696|135/2100||-2508|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7151|135/5655||-2508| GT:AD:DP:GQ 0/1:9:20:48 +17 41261233 . C T . . gnomad_exomes_an=31268;gnomad_exomes_hom=1604;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191449;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2683G>A|p.?|248/7088|135/5592||-2682|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2683G>A|p.?|188/7028|-7/5451||-2682|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2683G>A|p.?|242/3696|135/2100||-2682|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2683G>A|p.?|248/7151|135/5655||-2682| GT:AD:DP:GQ 0/1:12:27:48 +17 41263044 . A G . . gnomad_exomes_an=30560;gnomad_exomes_hom=1541;gnomad_exomes_het=6552;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191458;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-4494T>C|p.?|248/7088|135/5592||-4493|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4494T>C|p.?|188/7028|-7/5451||-4493|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4494T>C|p.?|242/3696|135/2100||-4493|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4494T>C|p.?|248/7151|135/5655||-4493| GT:AD:DP:GQ 0/1:7:14:48 +17 41263117 . C CA . . gnomad_exomes_an=17480;gnomad_exomes_hom=629;gnomad_exomes_het=3959;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-4568_135-4567insT|p.?|248/7088|135/5592||-4567|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4568_-7-4567insT|p.?|188/7028|-7/5451||-4567|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4568_135-4567insT|p.?|242/3696|135/2100||-4567|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4568_135-4567insT|p.?|248/7151|135/5655||-4567| GT:AD:DP:GQ 0/1:13:23:34 +17 41263566 . T C . . gnomad_exomes_an=29818;gnomad_exomes_hom=1603;gnomad_exomes_het=6680;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191462;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+4177A>G|p.?|247/7088|134/5592||4176|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5016A>G|p.?|188/7028|-7/5451||-5015|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+4177A>G|p.?|241/3696|134/2100||4176|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+4177A>G|p.?|247/7151|134/5655||4176| GT:AD:DP:GQ 0/1:11:19:48 +17 41264146 . G A . . gnomad_exomes_an=30782;gnomad_exomes_hom=1483;gnomad_exomes_het=6307;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191465;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3597C>T|p.?|247/7088|134/5592||3596|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5596C>T|p.?|188/7028|-7/5451||-5595|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3597C>T|p.?|241/3696|134/2100||3596|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3597C>T|p.?|247/7151|134/5655||3596| GT:AD:DP:GQ 0/1:13:20:45 +17 41264364 . A G . . gnomad_exomes_an=31320;gnomad_exomes_hom=1500;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191467;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3379T>C|p.?|247/7088|134/5592||3378|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5814T>C|p.?|188/7028|-7/5451||-5813|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3379T>C|p.?|241/3696|134/2100||3378|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3379T>C|p.?|247/7151|134/5655||3378| GT:AD:DP:GQ 0/1:8:24:45 +17 41264739 . C T . . gnomad_exomes_an=30908;gnomad_exomes_hom=3162;gnomad_exomes_het=7226;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255084;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3004G>A|p.?|247/7088|134/5592||3003|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6189G>A|p.?|188/7028|-7/5451||-6188|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3004G>A|p.?|241/3696|134/2100||3003|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3004G>A|p.?|247/7151|134/5655||3003| GT:AD:DP:GQ:PID 0|1:14:29:48:41264739 +17 41264740 . TGA T . . gnomad_exomes_an=31014;gnomad_exomes_hom=3159;gnomad_exomes_het=7229;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3001_134+3002delTC|p.?|247/7088|134/5592||3000|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6192_-7-6191delTC|p.?|188/7028|-7/5451||-6190|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3001_134+3002delTC|p.?|241/3696|134/2100||3000|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3001_134+3002delTC|p.?|247/7151|134/5655||3000| GT:AD:DP:GQ 0/1:14:30:48 +17 41264743 . CT C . . gnomad_exomes_an=30890;gnomad_exomes_hom=3155;gnomad_exomes_het=7228;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2999delA|p.?|247/7088|134/5592||2998|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6194delA|p.?|188/7028|-7/5451||-6193|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2999delA|p.?|241/3696|134/2100||2998|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2999delA|p.?|247/7151|134/5655||2998| GT:AD:DP:GQ:PID 0|1:14:29:48:41264739 +17 41264749 . C G . . gnomad_exomes_an=30892;gnomad_exomes_hom=3135;gnomad_exomes_het=7223;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256095;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2994G>C|p.?|247/7088|134/5592||2993|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6199G>C|p.?|188/7028|-7/5451||-6198|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2994G>C|p.?|241/3696|134/2100||2993|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2994G>C|p.?|247/7151|134/5655||2993| GT:AD:DP:GQ:PID 0|1:14:29:48:41264739 +17 41264750 . A T . . gnomad_exomes_an=30880;gnomad_exomes_hom=3136;gnomad_exomes_het=7219;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255162;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2993T>A|p.?|247/7088|134/5592||2992|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6200T>A|p.?|188/7028|-7/5451||-6199|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2993T>A|p.?|241/3696|134/2100||2992|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2993T>A|p.?|247/7151|134/5655||2992| GT:AD:DP:GQ:PID 0|1:14:29:48:41264739 +17 41264751 . A AGGG . . gnomad_exomes_an=30776;gnomad_exomes_hom=3136;gnomad_exomes_het=7222;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2991_134+2992insCCC|p.?|247/7088|134/5592||2991|,AGGG|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6202_-7-6201insCCC|p.?|188/7028|-7/5451||-6201|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2991_134+2992insCCC|p.?|241/3696|134/2100||2991|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2991_134+2992insCCC|p.?|247/7151|134/5655||2991| GT:AD:DP:GQ:PID 0|1:14:29:48:41264739 +17 41264753 . C T . . gnomad_exomes_an=30714;gnomad_exomes_hom=3130;gnomad_exomes_het=7189;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255582;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2990G>A|p.?|247/7088|134/5592||2989|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6203G>A|p.?|188/7028|-7/5451||-6202|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2990G>A|p.?|241/3696|134/2100||2989|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2990G>A|p.?|247/7151|134/5655||2989| GT:AD:DP:GQ:PID 0|1:14:27:48:41264739 +17 41264755 . TGAAAC T . . gnomad_exomes_an=30768;gnomad_exomes_hom=3130;gnomad_exomes_het=7187;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2983_134+2987delGTTTC|p.?|247/7088|134/5592||2982|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6210_-7-6206delGTTTC|p.?|188/7028|-7/5451||-6205|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2983_134+2987delGTTTC|p.?|241/3696|134/2100||2982|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2983_134+2987delGTTTC|p.?|247/7151|134/5655||2982| GT:AD:DP:GQ:PID 0|1:14:27:48:41264739 +17 41265776 . A G . . gnomad_exomes_an=31332;gnomad_exomes_hom=1615;gnomad_exomes_het=6700;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191470;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+1967T>C|p.?|247/7088|134/5592||1966|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7226T>C|p.?|188/7028|-7/5451||-7225|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1967T>C|p.?|241/3696|134/2100||1966|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1967T>C|p.?|247/7151|134/5655||1966| GT:AD:DP:GQ 0/1:23:37:44 +17 41266407 . C CT . . gnomad_exomes_an=22904;gnomad_exomes_hom=2326;gnomad_exomes_het=5197;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255595;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+1335_134+1336insA|p.?|247/7088|134/5592||1335|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7858_-7-7857insA|p.?|188/7028|-7/5451||-7857|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1335_134+1336insA|p.?|241/3696|134/2100||1335|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1335_134+1336insA|p.?|247/7151|134/5655||1335| GT:AD:DP:GQ 0/1:10:18:33 +17 41267050 . G A . . gnomad_exomes_an=31332;gnomad_exomes_hom=1619;gnomad_exomes_het=6726;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191477;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+693C>T|p.?|247/7088|134/5592||692|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-8500C>T|p.?|188/7028|-7/5451||-8499|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+693C>T|p.?|241/3696|134/2100||692|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+693C>T|p.?|247/7151|134/5655||692| GT:AD:DP:GQ 0/1:7:23:44 +17 41267518 . CA C . . gnomad_exomes_an=21564;gnomad_exomes_hom=937;gnomad_exomes_het=6113;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+224delT|p.?|247/7088|134/5592||223|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+8515delT|p.?|187/7028|-8/5451||8514|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+224delT|p.?|241/3696|134/2100||223|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+224delT|p.?|247/7151|134/5655||223| GT:AD:DP:GQ 0/1:11:19:35 +17 41268206 . A C . . gnomad_exomes_an=31210;gnomad_exomes_hom=1544;gnomad_exomes_het=6707;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191483;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-410T>G|p.?|194/7088|81/5592||-409|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7828T>G|p.?|187/7028|-8/5451||7827|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-410T>G|p.?|188/3696|81/2100||-409|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-410T>G|p.?|194/7151|81/5655||-409| GT:AD:DP:GQ:PID 0|1:13:22:46:41268206 +17 41268208 . C CT . . gnomad_exomes_an=31128;gnomad_exomes_hom=1385;gnomad_exomes_het=6554;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255730;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-413_81-412insA|p.?|194/7088|81/5592||-412|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7825_-8+7826insA|p.?|187/7028|-8/5451||7825|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-413_81-412insA|p.?|188/3696|81/2100||-412|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-413_81-412insA|p.?|194/7151|81/5655||-412| GT:AD:DP:GQ:PID 0|1:13:22:46:41268206 +17 41270229 . T G . . gnomad_exomes_an=31274;gnomad_exomes_hom=1606;gnomad_exomes_het=6696;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191491;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2433A>C|p.?|194/7088|81/5592||-2432|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5805A>C|p.?|187/7028|-8/5451||5804|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2433A>C|p.?|188/3696|81/2100||-2432|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2433A>C|p.?|194/7151|81/5655||-2432| GT:AD:DP:GQ 0/1:7:24:40 +17 41270277 . C T . . gnomad_exomes_an=31338;gnomad_exomes_hom=1513;gnomad_exomes_het=6416;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191493;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2481G>A|p.?|194/7088|81/5592||-2480|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5757G>A|p.?|187/7028|-8/5451||5756|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2481G>A|p.?|188/3696|81/2100||-2480|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2481G>A|p.?|194/7151|81/5655||-2480| GT:AD:DP:GQ 0/1:9:22:48 +17 41270463 . G A . . gnomad_exomes_an=30876;gnomad_exomes_hom=1578;gnomad_exomes_het=6604;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191497;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2667C>T|p.?|194/7088|81/5592||-2666|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5571C>T|p.?|187/7028|-8/5451||5570|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2667C>T|p.?|188/3696|81/2100||-2666|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2667C>T|p.?|194/7151|81/5655||-2666| GT:AD:DP:GQ 0/1:15:28:48 +17 41270666 . C A . . gnomad_exomes_an=31306;gnomad_exomes_hom=1500;gnomad_exomes_het=6413;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191498;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2870G>T|p.?|194/7088|81/5592||-2869|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5368G>T|p.?|187/7028|-8/5451||5367|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2870G>T|p.?|188/3696|81/2100||-2869|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2870G>T|p.?|194/7151|81/5655||-2869| GT:AD:DP:GQ 0/1:11:15:43 +17 41270778 . C CT . . gnomad_exomes_an=23434;gnomad_exomes_hom=923;gnomad_exomes_het=4562;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256051;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2983_81-2982insA|p.?|194/7088|81/5592||-2982|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5255_-8+5256insA|p.?|187/7028|-8/5451||5255|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2983_81-2982insA|p.?|188/3696|81/2100||-2982|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2983_81-2982insA|p.?|194/7151|81/5655||-2982| GT:AD:DP:GQ 0/1:11:16:14 +17 41271293 . GA G . . gnomad_exomes_an=26204;gnomad_exomes_hom=4218;gnomad_exomes_het=6049;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-3498delT|p.?|194/7088|81/5592||-3497|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+4740delT|p.?|187/7028|-8/5451||4739|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-3498delT|p.?|188/3696|81/2100||-3497|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-3498delT|p.?|194/7151|81/5655||-3497| GT:AD:DP:GQ 0/1:10:20:48 +17 41273095 . G A . . gnomad_exomes_an=27498;gnomad_exomes_hom=1472;gnomad_exomes_het=6401;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191505;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2939C>T|p.?|193/7088|80/5592||2938|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2939C>T|p.?|187/7028|-8/5451||2938|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2939C>T|p.?|187/3696|80/2100||2938|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2939C>T|p.?|193/7151|80/5655||2938| GT:AD:DP:GQ 0/1:12:20:47 +17 41273348 . T C . . gnomad_exomes_an=31018;gnomad_exomes_hom=4264;gnomad_exomes_het=6559;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191507;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2686A>G|p.?|193/7088|80/5592||2685|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2686A>G|p.?|187/7028|-8/5451||2685|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2686A>G|p.?|187/3696|80/2100||2685|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2686A>G|p.?|193/7151|80/5655||2685| GT:AD:DP:GQ 0/1:18:31:47 +17 41273379 . G C . . gnomad_exomes_an=30948;gnomad_exomes_hom=1487;gnomad_exomes_het=6371;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191508;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2655C>G|p.?|193/7088|80/5592||2654|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2655C>G|p.?|187/7028|-8/5451||2654|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2655C>G|p.?|187/3696|80/2100||2654|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2655C>G|p.?|193/7151|80/5655||2654| GT:AD:DP:GQ 0/1:19:33:47 +17 41273537 . A C . . gnomad_exomes_an=30662;gnomad_exomes_hom=1552;gnomad_exomes_het=6479;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191510;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2497T>G|p.?|193/7088|80/5592||2496|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2497T>G|p.?|187/7028|-8/5451||2496|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2497T>G|p.?|187/3696|80/2100||2496|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2497T>G|p.?|193/7151|80/5655||2496| GT:AD:DP:GQ 0/1:14:33:48 +17 41274778 . G A . . gnomad_exomes_an=31152;gnomad_exomes_hom=1594;gnomad_exomes_het=6661;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191511;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+1256C>T|p.?|193/7088|80/5592||1255|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1256C>T|p.?|187/7028|-8/5451||1255|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1256C>T|p.?|187/3696|80/2100||1255|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1256C>T|p.?|193/7151|80/5655||1255| GT:AD:DP:GQ 0/1:11:27:48 +17 41274906 . G A . . gnomad_exomes_an=28872;gnomad_exomes_hom=3662;gnomad_exomes_het=6225;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191514;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+1128C>T|p.?|193/7088|80/5592||1127|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1128C>T|p.?|187/7028|-8/5451||1127|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1128C>T|p.?|187/3696|80/2100||1127|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1128C>T|p.?|193/7151|80/5655||1127| GT:AD:DP:GQ 0/1:17:27:47 +17 41275081 . G GA . . gnomad_exomes_an=29534;gnomad_exomes_hom=1365;gnomad_exomes_het=6118;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191515;ANN=GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+952_80+953insT|p.?|193/7088|80/5592||952|,GA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+952_-8+953insT|p.?|187/7028|-8/5451||952|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+952_80+953insT|p.?|187/3696|80/2100||952|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+952_80+953insT|p.?|193/7151|80/5655||952| GT:AD:DP:GQ 0/1:10:22:47 +17 41275151 . G C . . gnomad_exomes_an=31080;gnomad_exomes_hom=1493;gnomad_exomes_het=6342;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191516;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+883C>G|p.?|193/7088|80/5592||882|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+883C>G|p.?|187/7028|-8/5451||882|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+883C>G|p.?|187/3696|80/2100||882|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+883C>G|p.?|193/7151|80/5655||882| GT:AD:DP:GQ 0/1:15:28:48 +17 41275366 . GTTTTTTT G . . ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+661_80+667delAAAAAAA|p.?|193/7088|80/5592||660|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+661_-8+667delAAAAAAA|p.?|187/7028|-8/5451||660|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+661_80+667delAAAAAAA|p.?|187/3696|80/2100||660|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+661_80+667delAAAAAAA|p.?|193/7151|80/5655||660| GT:AD:DP:GQ 0/1:10:21:48 +17 41275645 . A G . . gnomad_exomes_an=31292;gnomad_exomes_hom=1615;gnomad_exomes_het=6682;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001689724;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+389T>C|p.?|193/7088|80/5592||388|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+389T>C|p.?|187/7028|-8/5451||388|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+389T>C|p.?|187/3696|80/2100||388|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+389T>C|p.?|193/7151|80/5655||388| GT:AD:DP:GQ 0/1:15:32:48 +17 41276247 . A G . . gnomad_exomes_an=31318;gnomad_exomes_hom=1611;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001610389;ANN=G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-19-115T>C|p.?|95/7088|-19/5592||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-115T>C|p.?|89/7028|-106/5451||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-115T>C|p.?|89/3696|-19/2100||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-115T>C|p.?|95/7151|-19/5655||-114| GT:AD:DP:GQ 0/1:18:28:44 +17 41276348 . T C . . gnomad_exomes_an=31332;gnomad_exomes_hom=1609;gnomad_exomes_het=6706;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001711604;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-19-216A>G|p.?|95/7088|-19/5592||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-216A>G|p.?|89/7028|-106/5451||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-216A>G|p.?|89/3696|-19/2100||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-216A>G|p.?|95/7151|-19/5655||-215| GT:AD:DP:GQ 0/1:17:30:47 +17 41277187 . G C . . gnomad_exomes_an=29432;gnomad_exomes_hom=4088;gnomad_exomes_het=6345;gnomad_genomes_an=128296;gnomad_genomes_hom=11705;gnomad_genomes_het=29182;clinvar_clinsig=benign;clinvar_rcv=RCV001711453;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-20+101C>G|p.?|94/7088|-20/5592||100|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-107+107C>G|p.?|88/7028|-107/5451||106|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-20+107C>G|p.?|88/3696|-20/2100||106|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-20+101C>G|p.?|94/7151|-20/5655||100| GT:AD:DP:GQ 0/1:14:28:48 +MT 152 . T C . . . GT:GQ:AD:DP 1/1:98.13:2:10584 +MT 263 . A G . . . GT:GQ:AD:DP 1/1:98.13:0:7628 +MT 302 . A AC . . . GT:GQ:AD:DP 1/1:96.52:40:3536 +MT 310 . T TC . . . GT:GQ:AD:DP 1/1:96.88:7:3742 +MT 310 . T C . . . GT:GQ:AD:DP 0/1:21.54:7:3742 +MT 539 . T A . . . GT:GQ:AD:DP 0/1:21.53:6115:6405 +MT 596 . T A . . . GT:GQ:AD:DP 0/1:17.66:7690:7850 +MT 605 . T A . . . GT:GQ:AD:DP 0/1:21.53:5916:6058 +MT 610 . T A . . . GT:GQ:AD:DP 0/1:3.4:5986:6129 +MT 616 . T A . . . GT:GQ:AD:DP 0/1:0.12:6178:6261 +MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:7819 +MT 1438 . A G . . . GT:GQ:AD:DP 1/1:98.13:2:9170 +MT 2141 . T TAG . . . GT:GQ:AD:DP 0/1:20:6260:6286 +MT 2259 . C T . . . GT:GQ:AD:DP 1/1:98.13:3:7528 +MT 2645 . G A . . . GT:GQ:AD:DP 0/1:21.53:9159:9193 +MT 3572 . T G . . . GT:GQ:AD:DP 0/1:21.53:6937:7895 +MT 3572 . T A . . . GT:GQ:AD:DP 0/1:21.49:6937:7895 +MT 3577 . A C . . . GT:GQ:AD:DP 0/1:21.53:7519:7979 +MT 3578 . T A . . . GT:GQ:AD:DP 0/1:21.53:7041:7921 +MT 3578 . T G . . . GT:GQ:AD:DP 0/1:21.53:7041:7921 +MT 3583 . A C . . . GT:GQ:AD:DP 0/1:21.53:7746:8049 +MT 3590 . T A . . . GT:GQ:AD:DP 0/1:21.53:6859:7638 +MT 3593 . T G . . . GT:GQ:AD:DP 0/1:0.51:7844:8078 +MT 3595 . A C . . . GT:GQ:AD:DP 0/1:21.22:7958:8111 +MT 3599 . T A . . . GT:GQ:AD:DP 0/1:21.53:7408:7913 +MT 3605 . T A . . . GT:GQ:AD:DP 0/1:21.53:5371:5645 +MT 3614 . T A . . . GT:GQ:AD:DP 0/1:20.35:5553:5689 +MT 3631 . T A . . . GT:GQ:AD:DP 0/1:20.17:5740:5893 +MT 3633 . T A . . . GT:GQ:AD:DP 0/1:10.82:5829:5943 +MT 4434 . T G . . . GT:GQ:AD:DP 0/1:0.79:7711:7878 +MT 4491 . G A . . . GT:GQ:AD:DP 0/1:14.25:6096:6108 +MT 4745 . A G . . . GT:GQ:AD:DP:PID 1|1:94.1:0:4255:4745 +MT 4769 . A G . . . GT:GQ:AD:DP:PID 1|1:96.49:0:4115:4745 +MT 6518 . C T . . . GT:GQ:AD:DP 0/1:21.4:9464:9504 +MT 7337 . G A . . . GT:GQ:AD:DP 1/1:93.49:2:8855 +MT 8129 . A C . . . GT:GQ:AD:DP 0/1:20.26:7971:8173 +MT 8860 . A G . . . GT:GQ:AD:DP 1/1:91.87:0:4988 +MT 13326 . T C . . . GT:GQ:AD:DP 1/1:98.13:2:9163 +MT 13680 . C T . . . GT:GQ:AD:DP 1/1:98.13:1:5581 +MT 13680 . C G . . . GT:GQ:AD:DP 0/1:25.75:1:5581 +MT 13752 . T G . . . GT:GQ:AD:DP 0/1:21.51:4714:4779 +MT 13762 . T G . . . GT:GQ:AD:DP 0/1:21.53:4509:4689 +MT 13768 . T G . . . GT:GQ:AD:DP 0/1:21.53:4623:4778 +MT 13769 . T G . . . GT:GQ:AD:DP 0/1:21.53:4684:4799 +MT 14831 . G A . . . GT:GQ:AD:DP 1/1:98.13:3:8846 +MT 14831 . G C . . . GT:GQ:AD:DP 0/1:49.84:3:8846 +MT 14872 . C T . . . GT:GQ:AD:DP 1/1:98.13:5:6667 +MT 14918 . G A . . . GT:GQ:AD:DP 0/1:21.37:6570:6807 +MT 15326 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:7648 +MT 16023 . G A . . . GT:GQ:AD:DP 0/1:51.92:2572:9277 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap new file mode 100644 index 00000000..46e482c3 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap @@ -0,0 +1,56 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PID 0|1:11:17:43:41256074 +MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:7819 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap new file mode 100644 index 00000000..b6a5dbb0 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap @@ -0,0 +1,56 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PID 0|1:18:32:47:41256074 +MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:5608 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap new file mode 100644 index 00000000..aea06bdc --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap @@ -0,0 +1,60 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##SAMPLE= +##SAMPLE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 +17 41210126 . C CTAGCACTT . . gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974| GT:AD:DP:GQ 0/0:29:29:87 0/1:23:36:99 0/1:15:32:99 +MT 750 . A G . . . GT:AD:DP:GQ 1/1:0:2757:99 1/1:0:2392:99 1/1:0:1621:99 + diff --git a/src/sv/query/schema.rs b/src/sv/query/schema.rs index 89f1025e..d08d851c 100644 --- a/src/sv/query/schema.rs +++ b/src/sv/query/schema.rs @@ -1159,7 +1159,6 @@ where .filter_map(|token| { if let Some(caps) = re.captures(token) { let chrom = caps.name("chrom").unwrap().as_str().to_string(); - eprintln!("chrom: {}", &chrom); let chrom = if let Some(chrom) = chrom.strip_prefix("chr") { chrom.to_string() } else {