diff --git a/build.rs b/build.rs index 93fda381..44ebbf00 100644 --- a/build.rs +++ b/build.rs @@ -24,6 +24,7 @@ fn main() -> Result<(), anyhow::Error> { "annonars/gnomad/vep_gnomad2.proto", "annonars/gnomad/vep_gnomad3.proto", "annonars/helixmtdb/base.proto", + "annonars/regions/clingen.proto", ] .iter() .map(|f| root.join(f)) diff --git a/protos/annonars/regions/clingen.proto b/protos/annonars/regions/clingen.proto new file mode 100644 index 00000000..c9530922 --- /dev/null +++ b/protos/annonars/regions/clingen.proto @@ -0,0 +1,25 @@ +// Genomic region annotation with ClinGen information. + +syntax = "proto3"; + +package annonars.regions.clingen; + +import "annonars/genes/base.proto"; + +// Dosage pathogenicity region annotation. +message Region { + // ISCA ID + string isca_id = 1; + // ISCA Region Name + string isca_region_name = 2; + // Genomic locaion. + string genomic_location = 3; + // Haploinsufficiency score. + annonars.genes.base.ClingenDosageScore haploinsufficiency_score = 4; + // Triplosensitivity score. + annonars.genes.base.ClingenDosageScore triplosensitivity_score = 5; + // Haploinsufficiency Disease ID. + optional string haploinsufficiency_disease_id = 6; + // Haploinsufficiency Disease ID. + optional string triplosensitivity_disease_id = 7; +} diff --git a/src/genes/cli/data.rs b/src/genes/cli/data.rs index 7e896a8f..46dedcc8 100644 --- a/src/genes/cli/data.rs +++ b/src/genes/cli/data.rs @@ -104,9 +104,9 @@ pub mod clingen_gene { } } - impl From for crate::pbs::genes::ClingenDosageScore { + impl From for crate::pbs::genes::base::ClingenDosageScore { fn from(val: Score) -> Self { - use crate::pbs::genes::ClingenDosageScore::*; + use crate::pbs::genes::base::ClingenDosageScore::*; match val { Score::SufficientEvidence => SufficientEvidenceAvailable, Score::SomeEvidence => SomeEvidenceAvailable, @@ -1616,7 +1616,7 @@ pub mod shet { pub mod gtex { use serde::{Deserialize, Serialize}; - use crate::pbs::genes::{GtexTissue, GtexTissueDetailed}; + use crate::pbs::genes::base::{GtexTissue, GtexTissueDetailed}; /// GTEx V8 tissue types. #[derive(Debug, Clone, Serialize, Deserialize)] diff --git a/src/genes/cli/import.rs b/src/genes/cli/import.rs index bb777b41..583f6f51 100644 --- a/src/genes/cli/import.rs +++ b/src/genes/cli/import.rs @@ -371,7 +371,7 @@ fn load_domino(path: &str) -> Result, anyhow::Er } /// Convert from `data::*` records to protobuf records. -fn convert_record(record: data::Record) -> pbs::genes::Record { +fn convert_record(record: data::Record) -> pbs::genes::base::Record { let data::Record { acmg_sf, clingen, @@ -402,7 +402,7 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { variants_to_report, } = acmg_sf; - pbs::genes::AcmgSecondaryFindingRecord { + pbs::genes::base::AcmgSecondaryFindingRecord { hgnc_id, ensembl_gene_id, ncbi_gene_id, @@ -428,15 +428,15 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { triplosensitivity_disease_id, } = clingen; - pbs::genes::ClingenDosageRecord { + pbs::genes::base::ClingenDosageRecord { gene_symbol, ncbi_gene_id, genomic_location, - haploinsufficiency_score: Into::::into( + haploinsufficiency_score: Into::::into( clingen_gene::Score::try_from(haploinsufficiency_score) .expect("invalid haploinsufficiency score"), ) as i32, - triplosensitivity_score: Into::::into( + triplosensitivity_score: Into::::into( clingen_gene::Score::try_from(triplosensitivity_score) .expect("invalid triplosensitivity score"), ) as i32, @@ -548,7 +548,7 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { zfin_zebrafish_phenotype_tag, } = dbnsfp; - pbs::genes::DbnsfpRecord { + pbs::genes::base::DbnsfpRecord { gene_name, ensembl_gene, chr, @@ -680,7 +680,7 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { exac_oe_lof, } = gnomad_constraints; - pbs::genes::GnomadConstraintsRecord { + pbs::genes::base::GnomadConstraintsRecord { ensembl_gene_id, entrez_id, gene_symbol, @@ -762,7 +762,7 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { mane_select, } = hgnc; - Some(pbs::genes::HgncRecord { + Some(pbs::genes::base::HgncRecord { hgnc_id, symbol, name, @@ -796,7 +796,7 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { lsdb: lsdb .map(|lsdb| { lsdb.iter() - .map(|lsdb| pbs::genes::HgncLsdb { + .map(|lsdb| pbs::genes::base::HgncLsdb { name: lsdb.name.clone(), url: lsdb.url.clone(), }) @@ -831,14 +831,14 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { summary, rif_entries, } = ncbi; - pbs::genes::NcbiRecord { + pbs::genes::base::NcbiRecord { gene_id, summary, rif_entries: rif_entries .map(|rif_entries| { rif_entries .into_iter() - .map(|rif_entry| pbs::genes::RifEntry { + .map(|rif_entry| pbs::genes::base::RifEntry { pmids: rif_entry.pmids.unwrap_or_default(), text: rif_entry.text, }) @@ -850,11 +850,11 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { let omim = omim.map(|omim| { let omim::Record { hgnc_id, diseases } = omim; - pbs::genes::OmimRecord { + pbs::genes::base::OmimRecord { hgnc_id, omim_diseases: diseases .into_iter() - .map(|disease| pbs::genes::OmimTerm { + .map(|disease| pbs::genes::base::OmimTerm { omim_id: disease.omim_id, label: disease.label, }) @@ -864,11 +864,11 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { let orpha = orpha.map(|orpha| { let orpha::Record { hgnc_id, diseases } = orpha; - pbs::genes::OrphaRecord { + pbs::genes::base::OrphaRecord { hgnc_id, orpha_diseases: diseases .into_iter() - .map(|disease| pbs::genes::OrphaTerm { + .map(|disease| pbs::genes::base::OrphaTerm { orpha_id: disease.orpha_id, label: disease.label, }) @@ -882,7 +882,7 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { p_haplo, p_triplo, } = rcnv; - pbs::genes::RcnvRecord { + pbs::genes::base::RcnvRecord { hgnc_id, p_haplo, p_triplo, @@ -891,7 +891,7 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { let shet = shet.map(|shet| { let shet::Record { hgnc_id, s_het } = shet; - pbs::genes::ShetRecord { hgnc_id, s_het } + pbs::genes::base::ShetRecord { hgnc_id, s_het } }); let gtex = gtex.map(|gtex| { @@ -909,14 +909,14 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { tissue_detailed, tpms, } = record; - pbs::genes::GtexTissueRecord { + pbs::genes::base::GtexTissueRecord { tissue: tissue as i32, tissue_detailed: tissue_detailed as i32, tpms, } }) .collect::>(); - pbs::genes::GtexRecord { + pbs::genes::base::GtexRecord { hgnc_id, ensembl_gene_id, ensembl_gene_version, @@ -926,10 +926,10 @@ fn convert_record(record: data::Record) -> pbs::genes::Record { let domino = domino.map(|domino| { let domino::Record { gene_symbol, score } = domino; - pbs::genes::DominoRecord { gene_symbol, score } + pbs::genes::base::DominoRecord { gene_symbol, score } }); - pbs::genes::Record { + pbs::genes::base::Record { acmg_sf, clingen, dbnsfp, diff --git a/src/genes/cli/query.rs b/src/genes/cli/query.rs index a4c3a4d9..11fe7e7b 100644 --- a/src/genes/cli/query.rs +++ b/src/genes/cli/query.rs @@ -63,7 +63,7 @@ pub fn open_rocksdb_from_args( fn print_record( out_writer: &mut Box, output_format: common::cli::OutputFormat, - value: &genes::Record, + value: &genes::base::Record, ) -> Result<(), anyhow::Error> { match output_format { common::cli::OutputFormat::Jsonl => { @@ -79,13 +79,13 @@ pub fn query_for_gene( hgnc_id: &str, db: &rocksdb::DBWithThreadMode, cf_data: &Arc, -) -> Result, anyhow::Error> { +) -> Result, anyhow::Error> { let raw_value = db .get_cf(cf_data, hgnc_id.as_bytes()) .map_err(|e| anyhow::anyhow!("error while querying for HGNC ID {}: {}", hgnc_id, e))?; raw_value .map(|raw_value| { - genes::Record::decode(&mut std::io::Cursor::new(&raw_value)).map_err(|e| { + genes::base::Record::decode(&mut std::io::Cursor::new(&raw_value)).map_err(|e| { anyhow::anyhow!( "error while decoding gene record for HGNC ID {}: {}", hgnc_id, diff --git a/src/lib.rs b/src/lib.rs index 6858601a..deb2026c 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -19,6 +19,7 @@ pub mod gnomad_nuclear; pub mod gnomad_sv; pub mod helixmtdb; pub mod pbs; +pub mod regions; pub mod server; pub mod tsv; diff --git a/src/main.rs b/src/main.rs index 316567b1..bcd4141b 100644 --- a/src/main.rs +++ b/src/main.rs @@ -1,6 +1,6 @@ use annonars::{ clinvar_genes, clinvar_minimal, clinvar_sv, common, cons, db_utils, dbsnp, freqs, functional, - genes, gnomad_mtdna, gnomad_nuclear, gnomad_sv, helixmtdb, server, tsv, + genes, gnomad_mtdna, gnomad_nuclear, gnomad_sv, helixmtdb, regions, server, tsv, }; use anyhow::Error; use clap::{command, Args, Parser, Subcommand}; @@ -52,6 +52,8 @@ enum Commands { GnomadNuclear(GnomadNuclear), /// "gnomad-sv" sub commands GnomadSv(GnomadSv), + /// "regions" sub commands + Regions(Regions), /// "db-utils" sub commands DbUtils(DbUtils), /// "run-server" command. @@ -279,6 +281,23 @@ enum GnomadSvCommands { Query(gnomad_sv::cli::query::Args), } +/// Parsing of "regions" subcommands. +#[derive(Debug, Args, Clone)] +struct Regions { + /// The sub command to run + #[command(subcommand)] + command: RegionsCommands, +} + +/// Enum supporting the parsing of "regions *" subcommands. +#[derive(Debug, Subcommand, Clone)] +enum RegionsCommands { + /// "import" sub command + Import(regions::cli::import::Args), + /// "query" sub command + Query(regions::cli::query::Args), +} + /// Parsing of "db-utils" subcommands. #[derive(Debug, Args, Clone)] struct DbUtils { @@ -387,6 +406,10 @@ pub fn main() -> Result<(), anyhow::Error> { GnomadSvCommands::Import(args) => gnomad_sv::cli::import::run(&cli.common, args)?, GnomadSvCommands::Query(args) => gnomad_sv::cli::query::run(&cli.common, args)?, }, + Commands::Regions(args) => match &args.command { + RegionsCommands::Import(args) => regions::cli::import::run(&cli.common, args)?, + RegionsCommands::Query(args) => regions::cli::query::run(&cli.common, args)?, + }, Commands::DbUtils(args) => match &args.command { DbUtilsCommands::Copy(args) => db_utils::cli::copy::run(&cli.common, args)?, DbUtilsCommands::DumpMeta(args) => { diff --git a/src/pbs/genes.rs b/src/pbs/genes.rs index 209ff4fa..e04190ff 100644 --- a/src/pbs/genes.rs +++ b/src/pbs/genes.rs @@ -1,4 +1,7 @@ //! Code generate for protobufs by `prost-build`. -include!(concat!(env!("OUT_DIR"), "/annonars.genes.base.rs")); -include!(concat!(env!("OUT_DIR"), "/annonars.genes.base.serde.rs")); +/// Code generate for protobufs by `prost-build`. +pub mod base { + include!(concat!(env!("OUT_DIR"), "/annonars.genes.base.rs")); + include!(concat!(env!("OUT_DIR"), "/annonars.genes.base.serde.rs")); +} diff --git a/src/pbs/mod.rs b/src/pbs/mod.rs index f52ec7ab..fbe92a71 100644 --- a/src/pbs/mod.rs +++ b/src/pbs/mod.rs @@ -7,3 +7,4 @@ pub mod functional; pub mod genes; pub mod gnomad; pub mod helixmtdb; +pub mod regions; diff --git a/src/pbs/regions.rs b/src/pbs/regions.rs new file mode 100644 index 00000000..f912fd28 --- /dev/null +++ b/src/pbs/regions.rs @@ -0,0 +1,10 @@ +//! Code generate for protobufs by `prost-build`. + +/// Code generate for protobufs by `prost-build`. +pub mod clingen { + include!(concat!(env!("OUT_DIR"), "/annonars.regions.clingen.rs")); + include!(concat!( + env!("OUT_DIR"), + "/annonars.regions.clingen.serde.rs" + )); +} diff --git a/src/regions/cli/import.rs b/src/regions/cli/import.rs new file mode 100644 index 00000000..26966c75 --- /dev/null +++ b/src/regions/cli/import.rs @@ -0,0 +1,274 @@ +//! Import of genomic region data. + +use std::sync::Arc; + +use clap::Parser; +use prost::Message; + +use crate::{common, genes::cli::data::clingen_gene}; + +/// Helper data structures for reading CSV files. +pub mod clingen { + use std::{ + collections::HashMap, + io::{BufRead as _, BufReader}, + }; + + /// `ClinGen` region dosage sensitivity entry. + #[derive(Debug, PartialEq, serde::Deserialize, serde::Serialize)] + pub struct Region { + /// ISCA ID + #[serde(alias = "#ISCA ID")] + pub isca_id: String, + /// ISCA Region Name + #[serde(alias = "ISCA Region Name")] + pub isca_region_name: String, + /// Genomic location. + #[serde(alias = "Genomic Location")] + pub genomic_location: String, + /// Haploinsufficiency score. + #[serde(alias = "Haploinsufficiency Score", deserialize_with = "parse_score")] + pub haploinsufficiency_score: Option, + /// Triplosensitivity score. + #[serde(alias = "Triplosensitivity Score", deserialize_with = "parse_score")] + pub triplosensitivity_score: Option, + /// Haploinsufficiency Disease ID. + #[serde(alias = "Haploinsufficiency Disease ID")] + pub haploinsufficiency_disease_id: Option, + /// Haploinsufficiency Disease ID. + #[serde(alias = "Triplosensitivity Disease ID")] + pub triplosensitivity_disease_id: Option, + } + + /// Helper for parsing the scores which may have interesting values. + fn parse_score<'de, D>(d: D) -> Result, D::Error> + where + D: serde::Deserializer<'de>, + { + let tmp: String = serde::Deserialize::deserialize(d)?; + if tmp.is_empty() || tmp == "Not yet evaluated" || tmp == "-1" { + Ok(None) + } else { + Ok(Some(tmp.parse().map_err(serde::de::Error::custom)?)) + } + } + + /// Load ClinGen region CSV file. + /// + /// # Result + /// + /// A map from region ID to region. + pub fn load_clingen(path: &str) -> Result, anyhow::Error> { + tracing::info!(" loading ClinGen region curations from {}", path); + let mut result = HashMap::new(); + + // Construct reader and skip initial 5 lines. + let mut reader = std::fs::File::open(path) + .map_err(|e| anyhow::anyhow!("problem opening file: {}", e)) + .map(BufReader::new)?; + + { + let mut buf = String::new(); + for _ in 0..5 { + reader.read_line(&mut buf)?; + buf.clear(); + } + } + + let mut csv_reader = csv::ReaderBuilder::new() + .delimiter(b'\t') + .has_headers(true) + .flexible(true) + .from_reader(reader); + for record in csv_reader.deserialize() { + let record: Region = + record.map_err(|e| anyhow::anyhow!("problem parsing record: {}", e))?; + if genomic_location_to_interval(&record.genomic_location).is_err() { + tracing::warn!( + "skipping region with invalid genomic location: {}", + record.genomic_location + ); + continue; + } + result.insert(record.isca_id.clone(), record); + } + + Ok(result) + } + + /// Convert genomic location string to `bio::bio_types::genome::Interval`. + pub fn genomic_location_to_interval( + genomic_location: &str, + ) -> Result { + let mut parts = genomic_location.split(':'); + let chrom = parts.next().ok_or_else(|| { + anyhow::anyhow!( + "could not parse chromosome from genomic location: {}", + genomic_location + ) + })?; + let mut parts = parts + .next() + .ok_or_else(|| anyhow::anyhow!("could not parse region {}", genomic_location))? + .split('-'); + let begin = parts + .next() + .unwrap() + .parse::() + .map_err(|e| anyhow::anyhow!("could not parse start position from: {}", e))? + .saturating_sub(1); + let end = parts + .next() + .unwrap() + .parse::() + .map_err(|e| anyhow::anyhow!("could not parse end position from: {}", e))?; + Ok(bio::bio_types::genome::Interval::new( + chrom.to_string(), + begin..end, + )) + } +} + +/// Command line arguments for `regions import` sub command. +#[derive(Parser, Debug, Clone)] +#[command(about = "import region annotation data", long_about = None)] +pub struct Args { + /// Genome build to use in the build. + #[arg(long, value_enum)] + pub genome_release: common::cli::GenomeRelease, + /// Path to ClinGen region annotation file. + #[arg(long, required = true)] + pub path_in_clingen: String, + /// Path to output RocksDB directory. + #[arg(long)] + pub path_out_rocksdb: String, + + /// Name of the column family to import into. + #[arg(long, default_value = "regions")] + pub cf_name: String, + /// Optional path to RocksDB WAL directory. + #[arg(long)] + pub path_wal_dir: Option, +} + +/// Perform import of the TSV file. +fn tsv_import( + db: &rocksdb::DBWithThreadMode, + args: &Args, +) -> Result<(), anyhow::Error> { + let cf_data = db.cf_handle(&args.cf_name).unwrap(); + + let regions = clingen::load_clingen(&args.path_in_clingen)?; + + for (_, region) in regions { + let clingen::Region { + isca_id, + isca_region_name, + genomic_location, + haploinsufficiency_score, + triplosensitivity_score, + haploinsufficiency_disease_id, + triplosensitivity_disease_id, + } = region; + let haploinsufficiency_score = clingen_gene::Score::try_from(haploinsufficiency_score) + .map_err(|e| anyhow::anyhow!("problem parsing haplosensitivity score: {}", e))?; + let triplosensitivity_score = clingen_gene::Score::try_from(triplosensitivity_score) + .map_err(|e| anyhow::anyhow!("problem parsing triplosensitivity score: {}", e))?; + let region = crate::pbs::regions::clingen::Region { + isca_id, + isca_region_name, + genomic_location, + haploinsufficiency_score: haploinsufficiency_score as i32, + triplosensitivity_score: triplosensitivity_score as i32, + haploinsufficiency_disease_id, + triplosensitivity_disease_id, + }; + let key = format!("clingen:{}", ®ion.isca_id); + db.put_cf(&cf_data, key.as_bytes(), region.encode_to_vec())?; + } + + Ok(()) +} + +/// Implementation of `cons import` sub command. +pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> { + tracing::info!("Starting 'regions import' command"); + tracing::info!("common = {:#?}", &common); + tracing::info!("args = {:#?}", &args); + + // Open the RocksDB for writing. + tracing::info!("Opening RocksDB for writing ..."); + let before_opening_rocksdb = std::time::Instant::now(); + let options = rocksdb_utils_lookup::tune_options( + rocksdb::Options::default(), + args.path_wal_dir.as_ref().map(|s| s.as_ref()), + ); + let cf_names = &["meta", &args.cf_name]; + let db = Arc::new(rocksdb::DB::open_cf_with_opts( + &options, + common::readlink_f(&args.path_out_rocksdb)?, + cf_names + .iter() + .map(|name| (name.to_string(), options.clone())) + .collect::>(), + )?); + tracing::info!(" writing meta information"); + let cf_meta = db.cf_handle("meta").unwrap(); + db.put_cf(&cf_meta, "annonars-version", crate::VERSION)?; + db.put_cf( + &cf_meta, + "genome-release", + format!("{}", args.genome_release), + )?; + db.put_cf(&cf_meta, "db-name", "regions")?; + tracing::info!( + "... done opening RocksDB for writing in {:?}", + before_opening_rocksdb.elapsed() + ); + + tracing::info!("Importing TSV files ..."); + let before_import = std::time::Instant::now(); + tsv_import(&db, args)?; + tracing::info!( + "... done importing TSV files in {:?}", + before_import.elapsed() + ); + + tracing::info!("Running RocksDB compaction ..."); + let before_compaction = std::time::Instant::now(); + rocksdb_utils_lookup::force_compaction_cf(&db, cf_names, Some(" "), true)?; + tracing::info!( + "... done compacting RocksDB in {:?}", + before_compaction.elapsed() + ); + + tracing::info!("All done. Have a nice day!"); + Ok(()) +} + +#[cfg(test)] +mod test { + use super::*; + + use clap_verbosity_flag::Verbosity; + use temp_testdir::TempDir; + + #[test] + fn smoke_test_import() { + let tmp_dir = TempDir::default(); + let common = common::cli::Args { + verbose: Verbosity::new(1, 0), + }; + let args = Args { + genome_release: common::cli::GenomeRelease::Grch37, + path_in_clingen: String::from( + "tests/regions/clingen/ClinGen_region_curation_list_GRCh37.tsv", + ), + path_out_rocksdb: format!("{}", tmp_dir.join("out-rocksdb").display()), + cf_name: String::from("regions"), + path_wal_dir: None, + }; + + run(&common, &args).unwrap(); + } +} diff --git a/src/regions/cli/mod.rs b/src/regions/cli/mod.rs new file mode 100644 index 00000000..a6f4e656 --- /dev/null +++ b/src/regions/cli/mod.rs @@ -0,0 +1,4 @@ +//! Command line interface for genomic region import. + +pub mod import; +pub mod query; diff --git a/src/regions/cli/query.rs b/src/regions/cli/query.rs new file mode 100644 index 00000000..ba1a975e --- /dev/null +++ b/src/regions/cli/query.rs @@ -0,0 +1,468 @@ +//! Query genomic regions. + +use std::{io::Write, sync::Arc}; + +use bio::{ + bio_types::genome::AbstractInterval, data_structures::interval_tree::ArrayBackedIntervalTree, +}; +use prost::Message; + +use crate::common::{self, cli::extract_chrom, spdi}; + +/// Argument group for specifying accession or range. +#[derive(clap::Args, Debug, Clone, Default)] +#[group(required = true, multiple = false)] +pub struct ArgsQuery { + /// Query for all variants. + #[arg(long, group = "query")] + pub all: bool, + /// Query for variant with a specicic accession. + #[arg(long, group = "query")] + pub accession: Option, + /// Specify range to query for. + #[arg(long, group = "query")] + pub range: Option, +} + +/// Command line arguments for `regions clingen command. +#[derive(clap::Parser, Debug, Clone, Default)] +#[command(about = "query region data stored in RocksDB", long_about = None)] +pub struct Args { + /// Path to RocksDB directory with data. + #[arg(long)] + pub path_rocksdb: String, + /// Name of the column family to import into. + #[arg(long, default_value = "regions")] + pub cf_name: String, + /// Output file (default is stdout == "-"). + #[arg(long, default_value = "-")] + pub out_file: String, + /// Output format. + #[arg(long, default_value = "jsonl")] + pub out_format: common::cli::OutputFormat, + + /// Variant or position to query for. + #[command(flatten)] + pub query: ArgsQuery, +} + +/// Meta information as read from database. +#[derive(Debug)] +pub struct Meta { + /// Genome release of data in database. + pub genome_release: String, +} + +/// Open RocksDB given path and column family name for data and metadata. +pub fn open_rocksdb>( + path_rocksdb: P, + cf_data: &str, + cf_meta: &str, +) -> Result<(Arc>, Meta), anyhow::Error> { + tracing::info!("Opening RocksDB database at {} (cf={})...", path_rocksdb.as_ref().display(), &cf_data); + let before_open = std::time::Instant::now(); + let cf_names = &[cf_meta, cf_data]; + let db = Arc::new(rocksdb::DB::open_cf_for_read_only( + &rocksdb::Options::default(), + common::readlink_f(&path_rocksdb)?, + cf_names, + true, + )?); + tracing::info!(" reading meta information"); + let meta = { + let cf_meta = db.cf_handle(cf_meta).unwrap(); + let genome_release = String::from_utf8( + db.get_cf(&cf_meta, "genome-release")? + .ok_or_else(|| anyhow::anyhow!("missing value meta:genome-release"))?, + )?; + Meta { genome_release } + }; + + tracing::info!(" meta:genome-release = {}", &meta.genome_release); + tracing::info!( + "... opening RocksDB database took {:?}", + before_open.elapsed() + ); + + Ok((db, meta)) +} + +/// Open RocksDB database from command line arguments. +pub fn open_rocksdb_from_args( + args: &Args, +) -> Result<(Arc>, Meta), anyhow::Error> { + open_rocksdb(&args.path_rocksdb, &args.cf_name, "meta") +} + +/// Enumeration for the different record types that we have. +#[derive(Debug, Clone, PartialEq, serde::Serialize, serde::Deserialize)] +#[serde(rename_all = "snake_case")] +pub enum Record { + /// ClinGen dosage record. + ClingenDosage(crate::pbs::regions::clingen::Region), +} + +/// The necessary data for the tree construction. +#[derive(Debug)] +pub struct TreeData { + /// The chromosome. + pub chromosome: String, + /// The start position. + pub start: u32, + /// The stop position. + pub stop: u32, +} + +impl Record { + fn tree_data(&self) -> TreeData { + match self { + Record::ClingenDosage(record) => { + let interval = + super::import::clingen::genomic_location_to_interval(&record.genomic_location) + .expect("could not decode genomic location"); + TreeData { + chromosome: interval.contig().to_string(), + start: interval.range().start as u32, + stop: interval.range().end as u32, + } + } + } + } +} + +/// Write a single record to `out_writer`. +fn print_record( + out_writer: &mut Box, + output_format: common::cli::OutputFormat, + value: &Record, +) -> Result<(), anyhow::Error> { + match (output_format, value) { + (common::cli::OutputFormat::Jsonl, Record::ClingenDosage(record)) => { + writeln!(out_writer, "{}", serde_json::to_string(record)?)? + } + } + + Ok(()) +} + +/// Decode a key/record. +fn decode_record(key: &[u8], data: &[u8]) -> Result { + Ok(if key.starts_with(b"clingen:") { + Record::ClingenDosage(crate::pbs::regions::clingen::Region::decode( + &mut std::io::Cursor::new(&data), + )?) + } else { + let key = std::str::from_utf8(key).unwrap_or("COULD_NOT_DECODE_KEY"); + anyhow::bail!("unknown record type from key: {}", key); + }) +} + +/// Iterate all regions and print to `out_writer`. +fn print_all( + out_writer: &mut Box, + out_format: common::cli::OutputFormat, + db: &rocksdb::DBWithThreadMode, + cf_data: &Arc, +) -> Result<(), anyhow::Error> { + tracing::info!("dumping all records..."); + + let mut iter = db.raw_iterator_cf(cf_data); + iter.seek(b""); + while iter.valid() { + if let (Some(raw_key), Some(raw_value)) = (iter.key(), iter.value()) { + print_record(out_writer, out_format, &decode_record(raw_key, raw_value)?)?; + iter.next(); + } else { + break; + } + } + + tracing::info!("... done dumping all records"); + Ok(()) +} + +/// Helper data structure that provides per-chromosome interval trees for querying. +pub struct IntervalTrees { + /// Per-chromosome interval trees. + trees: rustc_hash::FxHashMap>>, + /// Backing RocksDB. + db: Arc>, + /// Name of column family with data. + cf_data_name: String, + /// Meta information from database. + meta: Meta, +} + +impl IntervalTrees { + /// Construct new per-contig interval trees. + /// + /// This will read all records from the database and build the interval trees. + /// + /// # Arguments + /// + /// * `db` - Database to read from. + /// * `cf_data_name` - Name of column family with data. + /// * `meta` - Meta information from database. + /// + /// # Returns + /// + /// * `Self` - New instance. + /// + /// # Errors + /// + /// * If reading from the database fails. + pub fn with_db( + db: Arc>, + cf_data_name: &str, + meta: Meta, + ) -> Result { + let cf_data = db.cf_handle(cf_data_name).ok_or_else(|| { + anyhow::anyhow!("no column family with name {:?} found", cf_data_name) + })?; + Ok(Self { + trees: Self::build_trees(db.clone(), cf_data.clone())?, + db: db.clone(), + cf_data_name: cf_data_name.to_string(), + meta, + }) + } + + /// Build the interval trees. + fn build_trees( + db: Arc>, + cf_data: Arc, + ) -> Result>>, anyhow::Error> + { + let mut result: rustc_hash::FxHashMap>> = + rustc_hash::FxHashMap::default(); + + // Obtain iterator and seek to start. + let mut iter = db.raw_iterator_cf(&cf_data); + iter.seek(b""); + while iter.valid() { + if let (Some(raw_key), Some(raw_value)) = (iter.key(), iter.value()) { + let record = decode_record(raw_key, raw_value) + .map_err(|e| anyhow::anyhow!("failed to decode record: {}", e))?; + let key = iter.key().unwrap().to_vec(); + tracing::trace!("iterator at {:?} => {:?}", &key, &record); + + let TreeData { + chromosome, + start, + stop, + } = record.tree_data(); + + let interval = (start as u64)..(stop as u64); + let chrom = chromosome.strip_prefix("chr").unwrap_or(&chromosome); + tracing::trace!("contig = {} / {:?} / {:?}", &chrom, &interval, &key); + result + .entry(chrom.to_string()) + .or_default() + .insert(interval, key); + assert!(result.contains_key(chrom)); + + iter.next(); + } else { + break; + } + } + + result.values_mut().for_each(|tree| tree.index()); + + Ok(result) + } + + /// Query for a range. + pub fn query(&self, range: &spdi::Range) -> Result, anyhow::Error> { + tracing::trace!("query for {:?}", &range); + 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) + })?; + let interval = (range.start as u64 )..(range.end as u64); + let mut result = Vec::new(); + if let Some(tree) = self.trees.get(&contig) { + for entry in tree.find(&interval) { + tracing::info!("found entry: {:?}", &entry); + if let Some(raw_value) = self.db.get_cf(&cf_data, entry.data())? { + result.push(decode_record(&entry.data(), &raw_value)?); + } + } + } else { + tracing::warn!("unknown contig: {:?}", &contig); + } + + Ok(result) + } +} + +/// Implementation of `tsv query` sub command. +pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> { + tracing::info!("Starting 'region query' command"); + tracing::info!("common = {:#?}", &common); + tracing::info!("args = {:#?}", &args); + + let (db, meta) = open_rocksdb_from_args(args)?; + let cf_data = db.cf_handle(&args.cf_name).unwrap(); + + // Obtain writer to output. + let mut out_writer = match args.out_file.as_ref() { + "-" => Box::new(std::io::stdout()) as Box, + out_file => { + let path = std::path::Path::new(out_file); + Box::new(std::fs::File::create(path).unwrap()) as Box + } + }; + + tracing::info!("Running query..."); + let before_query = std::time::Instant::now(); + if let Some(range) = args.query.range.as_ref() { + tracing::info!("for range {:?}", &range); + tracing::info!("Building interval trees..."); + let trees = IntervalTrees::with_db(db.clone(), &args.cf_name, meta) + .map_err(|e| anyhow::anyhow!("failed to build interval trees: {}", e))?; + tracing::info!("... done building interval trees"); + tracing::info!("Running query..."); + let records = trees + .query(range) + .map_err(|e| anyhow::anyhow!("failed to query interval trees: {}", e))?; + for record in &records { + print_record(&mut out_writer, args.out_format, record)?; + } + tracing::info!("... done running query"); + } else if let Some(accession) = args.query.accession.as_ref() { + tracing::info!("for accession {}", accession); + let buf = db + .get_cf(&cf_data, accession.as_bytes()) + .map_err(|e| anyhow::anyhow!("failed to query RocksDB: {}", e))?; + if let Some(buf) = buf { + let record = decode_record(accession.as_bytes(), &buf)?; + print_record(&mut out_writer, args.out_format, &record)?; + } else { + tracing::warn!("no record found for accession {}", accession); + } + tracing::info!("... done running query"); + } else if args.query.all { + tracing::info!("for all"); + print_all(&mut out_writer, args.out_format, &db, &cf_data)?; + } else { + unreachable!(); + } + tracing::info!("... done querying in {:?}", before_query.elapsed()); + + tracing::info!("All done. Have a nice day!"); + Ok(()) +} + +#[cfg(test)] +mod test { + use std::str::FromStr as _; + use temp_testdir::TempDir; + + use crate::common; + + #[rstest::fixture] + fn args_args_temp() -> (common::cli::Args, super::Args, TempDir) { + let temp = TempDir::default(); + let common = common::cli::Args { + verbose: clap_verbosity_flag::Verbosity::new(1, 0), + }; + let args = super::Args { + cf_name: String::from("regions"), + out_file: temp.join("out").to_string_lossy().to_string(), + out_format: common::cli::OutputFormat::Jsonl, + ..Default::default() + }; + + (common, args, temp) + } + + #[tracing_test::traced_test] + #[rstest::rstest] + #[case("tests/regions/clingen/rocksdb", "clingen")] + fn smoke_query_region_all( + #[case] path_rocksdb: &str, + #[case] label: &str, + args_args_temp: (common::cli::Args, super::Args, TempDir), + ) -> Result<(), anyhow::Error> { + crate::common::set_snapshot_suffix!("{}", &label); + + let (common, args, _temp) = args_args_temp; + let args = super::Args { + path_rocksdb: path_rocksdb.to_string(), + query: super::ArgsQuery { + all: true, + ..Default::default() + }, + ..args + }; + super::run(&common, &args)?; + let out_data = std::fs::read_to_string(&args.out_file)?; + insta::assert_snapshot!(&out_data); + + Ok(()) + } + + #[tracing_test::traced_test] + #[rstest::rstest] + #[case("tests/regions/clingen/rocksdb", "clingen:ISCA-46733", "clingen-ISCA-46733")] + fn smoke_query_var_accession( + #[case] path_rocksdb: &str, + #[case] accession: &str, + #[case] label: &str, + args_args_temp: (common::cli::Args, super::Args, TempDir), + ) -> Result<(), anyhow::Error> { + crate::common::set_snapshot_suffix!("{}", &label); + + let (common, args, _temp) = args_args_temp; + let args = super::Args { + path_rocksdb: path_rocksdb.to_string(), + query: super::ArgsQuery { + accession: Some(accession.to_string()), + ..Default::default() + }, + ..args + }; + super::run(&common, &args)?; + let out_data = std::fs::read_to_string(&args.out_file)?; + insta::assert_snapshot!(&out_data); + + Ok(()) + } + + #[tracing_test::traced_test] + #[rstest::rstest] + #[case( + "tests/regions/clingen/rocksdb", + "chrX:47880294:47952112", + "clingen-some" + )] + #[case( + "tests/regions/clingen/rocksdb", + "chr1:47880294:47952112", + "clingen-none" + )] + fn smoke_query_range( + #[case] path_rocksdb: &str, + #[case] range: &str, + #[case] label: &str, + args_args_temp: (common::cli::Args, super::Args, TempDir), + ) -> Result<(), anyhow::Error> { + crate::common::set_snapshot_suffix!("{}", &label); + + let (common, args, _temp) = args_args_temp; + let args = super::Args { + path_rocksdb: path_rocksdb.to_string(), + query: super::ArgsQuery { + range: Some(crate::common::spdi::Range::from_str(range)?), + ..Default::default() + }, + ..args + }; + super::run(&common, &args)?; + let out_data = std::fs::read_to_string(&args.out_file)?; + insta::assert_snapshot!(&out_data); + + Ok(()) + } +} diff --git a/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_range@clingen-none.snap b/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_range@clingen-none.snap new file mode 100644 index 00000000..c3cfdc46 --- /dev/null +++ b/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_range@clingen-none.snap @@ -0,0 +1,5 @@ +--- +source: src/regions/cli/query.rs +expression: "&out_data" +--- + diff --git a/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_range@clingen-some.snap b/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_range@clingen-some.snap new file mode 100644 index 00000000..a7031f0e --- /dev/null +++ b/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_range@clingen-some.snap @@ -0,0 +1,6 @@ +--- +source: src/regions/cli/query.rs +expression: "&out_data" +--- +{"iscaId":"ISCA-46735","iscaRegionName":"Xp11.23 population region (DGV_Gold_Standard_June_2021_gssvL136075)","genomicLocation":"chrX:47880294-47952112","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE"} + diff --git a/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_region_all@clingen.snap b/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_region_all@clingen.snap new file mode 100644 index 00000000..07ec6e55 --- /dev/null +++ b/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_region_all@clingen.snap @@ -0,0 +1,518 @@ +--- +source: src/regions/cli/query.rs +expression: "&out_data" +--- +{"iscaId":"ISCA-37390","iscaRegionName":"5p15 terminal (Cri du chat syndrome) region","genomicLocation":"chr5:37693-11347262","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_SOME_EVIDENCE_AVAILABLE","haploinsufficiencyDiseaseId":"MONDO:0007404"} +{"iscaId":"ISCA-37392","iscaRegionName":"7q11.23 recurrent (Williams-Beuren syndrome) region (includes ELN)","genomicLocation":"chr7:72744455-74142510","haploinsufficiencyDiseaseId":"MONDO:0008678","triplosensitivityDiseaseId":"MONDO:0012342"} +{"iscaId":"ISCA-37393","iscaRegionName":"22q11.21 recurrent (Cat eye syndrome) region (includes CECR2)","genomicLocation":"chr22:17392953-18591860","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE","triplosensitivityDiseaseId":"MONDO:0007276"} +{"iscaId":"ISCA-37394","iscaRegionName":"2q37.3 terminal region (includes HDAC4)","genomicLocation":"chr2:239954693-242930600","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE","haploinsufficiencyDiseaseId":"MONDO:0010886"} +{"iscaId":"ISCA-37396","iscaRegionName":"15q24 recurrent region (LCR A-LCR D) (includes SIN3A)","genomicLocation":"chr15:72963715-75972909","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE","haploinsufficiencyDiseaseId":"MONDO:0013672"} +{"iscaId":"ISCA-37397","iscaRegionName":"22q11.2 recurrent region (distal type I, D-E/F)","genomicLocation":"chr22:21917117-23649111","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE","haploinsufficiencyDiseaseId":"MONDO:0012740"} +{"iscaId":"ISCA-37400","iscaRegionName":"16p11.2 recurrent region (proximal, BP4-BP5) (includes TBX6)","genomicLocation":"chr16:29649997-30199852","haploinsufficiencyDiseaseId":"MONDO:0012756","triplosensitivityDiseaseId":"MONDO:0013847"} +{"iscaId":"ISCA-37401","iscaRegionName":"11p13 (WAGR syndrome) region","genomicLocation":"chr11:31803509-32510988","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE","haploinsufficiencyDiseaseId":"MONDO:0008681"} +{"iscaId":"ISCA-37404","iscaRegionName":"15q11.2q13 recurrent (PWS/AS) region (Class 1, BP1-BP3)","genomicLocation":"chr15:22832519-28379874","haploinsufficiencyDiseaseId":"MONDO:0008300","triplosensitivityDiseaseId":"MONDO:0012081"} +{"iscaId":"ISCA-37405","iscaRegionName":"2q13 recurrent region (includes NPHP1)","genomicLocation":"chr2:110862108-110983703","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_RECESSIVE","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY"} +{"iscaId":"ISCA-37406","iscaRegionName":"16p13.3 region (includes CREBBP)","genomicLocation":"chr16:3775056-3930121","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE","haploinsufficiencyDiseaseId":"MONDO:0012519"} +{"iscaId":"ISCA-37408","iscaRegionName":"2p15p16.1 region (includes BCL11A)","genomicLocation":"chr2:59139200-62488871","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE","haploinsufficiencyDiseaseId":"MONDO:0012916"} +{"iscaId":"ISCA-37409","iscaRegionName":"16p12.2 recurrent region (proximal) (includes EEF2K, CDR2)","genomicLocation":"chr16:21948445-22430804","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_SOME_EVIDENCE_AVAILABLE","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE"} +{"iscaId":"ISCA-37411","iscaRegionName":"15q13.3 recurrent region (BP4-BP5) (includes CHRNA7)","genomicLocation":"chr15:31192889-32445405","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE","haploinsufficiencyDiseaseId":"MONDO:0012774"} +{"iscaId":"ISCA-37415","iscaRegionName":"16p13.11 recurrent region (BP2-BP3) (includes MYH11)","genomicLocation":"chr16:15511711-16292265","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_SOME_EVIDENCE_AVAILABLE"} +{"iscaId":"ISCA-37417","iscaRegionName":"Xp22.31 recurrent region (includes STS)","genomicLocation":"chrX:6455812-8124954","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY","haploinsufficiencyDiseaseId":"MONDO:0010622"} +{"iscaId":"ISCA-37418","iscaRegionName":"17p11.2 recurrent (SMS/PLS) region (includes RAI1)","genomicLocation":"chr17:16810028-20213202","haploinsufficiencyDiseaseId":"MONDO:0008434","triplosensitivityDiseaseId":"MONDO:0012574"} +{"iscaId":"ISCA-37420","iscaRegionName":"17q21.3 recurrent region (includes KANSL1)","genomicLocation":"chr17:43705166-44164880","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE","haploinsufficiencyDiseaseId":"MONDO:0012496"} +{"iscaId":"ISCA-37421","iscaRegionName":"1q21.1 recurrent region (BP3-BP4, distal) (includes GJA5)","genomicLocation":"chr1:146577486-147394506","haploinsufficiencyDiseaseId":"MONDO:0012914","triplosensitivityDiseaseId":"MONDO:0012915"} +{"iscaId":"ISCA-37423","iscaRegionName":"8p23.1 recurrent region (includes GATA4)","genomicLocation":"chr8:8100064-11766329","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_SOME_EVIDENCE_AVAILABLE"} +{"iscaId":"ISCA-37424","iscaRegionName":"10q22.3q23.2 recurrent region (includes BMPR1A)","genomicLocation":"chr10:81682843-88739388","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE"} +{"iscaId":"ISCA-37425","iscaRegionName":"5q35 recurrent (Sotos syndrome) region (includes NSD1)","genomicLocation":"chr5:175728979-177047793","haploinsufficiencyDiseaseId":"MONDO:0019349"} +{"iscaId":"ISCA-37428","iscaRegionName":"1q21.1 recurrent (TAR syndrome) region (proximal, BP2-BP3) (includes RBM8A)","genomicLocation":"chr1:145386507-145748064","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE","haploinsufficiencyDiseaseId":"MONDO:0010121"} +{"iscaId":"ISCA-37429","iscaRegionName":"4p16.3 terminal (Wolf-Hirschhorn syndrome) region","genomicLocation":"chr4:331568-2010962","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_SOME_EVIDENCE_AVAILABLE","haploinsufficiencyDiseaseId":"MONDO:0008684"} +{"iscaId":"ISCA-37430","iscaRegionName":"17p13.3 (Miller-Dieker syndrome) region (includes YWHAE and PAFAH1B1)","genomicLocation":"chr17:1247833-2588909","haploinsufficiencyDiseaseId":"MONDO:0009532","triplosensitivityDiseaseId":"MONDO:0013182"} +{"iscaId":"ISCA-37431","iscaRegionName":"17q11.2 recurrent region (includes NF1)","genomicLocation":"chr17:29097069-30264027","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_SOME_EVIDENCE_AVAILABLE","haploinsufficiencyDiseaseId":"MONDO:0013357","triplosensitivityDiseaseId":"MONDO:0030032"} +{"iscaId":"ISCA-37432","iscaRegionName":"17q12 recurrent (RCAD syndrome) region (includes HNF1B)","genomicLocation":"chr17:34815072-36192489","haploinsufficiencyDiseaseId":"MONDO:0013797","triplosensitivityDiseaseId":"MONDO:0013796"} +{"iscaId":"ISCA-37433","iscaRegionName":"22q11.2 recurrent (DGS/VCFS) region (proximal, A-B) (includes TBX1)","genomicLocation":"chr22:18912231-20287208","haploinsufficiencyDiseaseId":"MONDO:0008564","triplosensitivityDiseaseId":"MONDO:0012020"} +{"iscaId":"ISCA-37434","iscaRegionName":"1p36 terminal region (includes GABRD)","genomicLocation":"chr1:834083-6289973","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_SOME_EVIDENCE_AVAILABLE","haploinsufficiencyDiseaseId":"MONDO:0011929"} +{"iscaId":"ISCA-37436","iscaRegionName":"17p12 recurrent 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(DGV_Gold_Standard_June_2021_gssvL77050)","genomicLocation":"chr22:21866876-21909287","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE"} +{"iscaId":"ISCA-46732","iscaRegionName":"22q11.23 population region (DGV_Gold_Standard_June_2021_gssvG24415)","genomicLocation":"chr22:25703259-25785235","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY"} +{"iscaId":"ISCA-46733","iscaRegionName":"Xq24 population region (DGV_Gold_Standard_June_2021_gssvG41158)","genomicLocation":"chrX:120006512-120123897","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY"} +{"iscaId":"ISCA-46734","iscaRegionName":"Xq28 population region (DGV_Gold_Standard_June_2021_gssvG41365)","genomicLocation":"chrX:153409846-153460630","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY"} +{"iscaId":"ISCA-46735","iscaRegionName":"Xp11.23 population region (DGV_Gold_Standard_June_2021_gssvL136075)","genomicLocation":"chrX:47880294-47952112","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE"} +{"iscaId":"ISCA-46736","iscaRegionName":"Xq21.1 population region (DGV_Gold_Standard_June_2021_gssvL136501)","genomicLocation":"chrX:76137628-76141022","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE"} +{"iscaId":"ISCA-46737","iscaRegionName":"Xq27.3 population region (DGV_Gold_Standard_June_2021_gssvL137799)","genomicLocation":"chrX:142601775-142800327","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE"} +{"iscaId":"ISCA-46738","iscaRegionName":"Yq11.223 population region (DGV_Gold_Standard_June_2021_gssvL138419)","genomicLocation":"chrY:24361866-24465171","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE"} +{"iscaId":"ISCA-46739","iscaRegionName":"Yq11.223 population region (DGV_Gold_Standard_June_2021_gssvL138428)","genomicLocation":"chrY:25853189-26146959","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE"} +{"iscaId":"ISCA-46741","iscaRegionName":"9p24.3 Region (includes DMRT1)","genomicLocation":"chr9:1-1982069","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_SOME_EVIDENCE_AVAILABLE","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE","haploinsufficiencyDiseaseId":"MONDO:0002145"} +{"iscaId":"ISCA-46742","iscaRegionName":"7p22.1 region (includes ACTB)","genomicLocation":"chr7:5536848-5799722","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE","haploinsufficiencyDiseaseId":"MONDO:0000508","triplosensitivityDiseaseId":"MONDO:0100038"} +{"iscaId":"ISCA-46743","iscaRegionName":"Xq25 region (includes STAG2)","genomicLocation":"chrX:123034319-123236519","triplosensitivityDiseaseId":"MONDO:0100038"} +{"iscaId":"ISCA-46747","iscaRegionName":"22q11.2 recurrent region (distal type III, E/F-H) (includes SMARCB1)","genomicLocation":"chr22:23119415-24994433","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_LITTLE_EVIDENCE"} + diff --git a/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_var_accession@clingen-ISCA-46733.snap b/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_var_accession@clingen-ISCA-46733.snap new file mode 100644 index 00000000..60a13822 --- /dev/null +++ b/src/regions/cli/snapshots/annonars__regions__cli__query__test__smoke_query_var_accession@clingen-ISCA-46733.snap @@ -0,0 +1,6 @@ +--- +source: src/regions/cli/query.rs +expression: "&out_data" +--- +{"iscaId":"ISCA-46733","iscaRegionName":"Xq24 population region (DGV_Gold_Standard_June_2021_gssvG41158)","genomicLocation":"chrX:120006512-120123897","haploinsufficiencyScore":"CLINGEN_DOSAGE_SCORE_NO_EVIDENCE_AVAILABLE","triplosensitivityScore":"CLINGEN_DOSAGE_SCORE_UNLIKELY"} + diff --git a/src/regions/mod.rs b/src/regions/mod.rs new file mode 100644 index 00000000..74d15b15 --- /dev/null +++ b/src/regions/mod.rs @@ -0,0 +1,3 @@ +//! Genomic region annotation, e.g., with ClinGen. + +pub mod cli; diff --git a/src/server/actix_server/genes_info.rs b/src/server/actix_server/genes_info.rs index bd57c9ea..80abf00c 100644 --- a/src/server/actix_server/genes_info.rs +++ b/src/server/actix_server/genes_info.rs @@ -29,7 +29,7 @@ struct Request { struct Container { // TODO: add data version /// The resulting gene information. - pub genes: indexmap::IndexMap, + pub genes: indexmap::IndexMap, } /// Query for annotations for one variant. @@ -55,7 +55,7 @@ async fn handle( .get_cf(&cf_genes, hgnc_id) .map_err(|e| CustomError::new(anyhow::anyhow!("problem querying database: {}", e)))? .ok_or_else(|| CustomError::new(anyhow::anyhow!("no such gene: {}", hgnc_id)))?; - let record = genes::Record::decode(std::io::Cursor::new(raw_buf)) + let record = genes::base::Record::decode(std::io::Cursor::new(raw_buf)) .map_err(|e| CustomError::new(anyhow::anyhow!("problem decoding value: {}", e)))?; genes.insert(hgnc_id.to_string(), record); } diff --git a/src/server/mod.rs b/src/server/mod.rs index 7a8d2746..70c87cd7 100644 --- a/src/server/mod.rs +++ b/src/server/mod.rs @@ -271,10 +271,10 @@ fn extract_gene_names( iter.seek(b""); while iter.valid() { if let Some(iter_value) = iter.value() { - let record = genes::Record::decode(std::io::Cursor::new(iter_value))?; - let genes::Record { hgnc, .. } = record; + let record = genes::base::Record::decode(std::io::Cursor::new(iter_value))?; + let genes::base::Record { hgnc, .. } = record; if let Some(hgnc) = hgnc { - let genes::HgncRecord { + let genes::base::HgncRecord { hgnc_id, symbol, name, diff --git a/tests/regions/bootstrap.sh b/tests/regions/bootstrap.sh new file mode 100644 index 00000000..83a31144 --- /dev/null +++ b/tests/regions/bootstrap.sh @@ -0,0 +1,8 @@ +#!/usr/bin/env bash + +rm -rf tests/regions/clingen/rocksdb + +cargo run -- regions import \ + --genome-release grch37 \ + --path-in-clingen tests/regions/clingen/ClinGen_region_curation_list_GRCh37.tsv \ + --path-out-rocksdb tests/regions/clingen/rocksdb diff --git a/tests/regions/clingen/ClinGen_region_curation_list_GRCh37.tsv b/tests/regions/clingen/ClinGen_region_curation_list_GRCh37.tsv new file mode 100644 index 00000000..ebde8cbf --- /dev/null +++ b/tests/regions/clingen/ClinGen_region_curation_list_GRCh37.tsv @@ -0,0 +1,520 @@ +#ClinGen Region Curation Results +#14 Nov,2023 +#Genomic Locations are reported on GRCh37 (hg19): GCF_000001405.13 +#https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen +#to create link: https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/clingen_region.cgi?id=key +#ISCA ID ISCA Region Name cytoBand Genomic Location Haploinsufficiency Score Haploinsufficiency Description Haploinsufficiency PMID1 Haploinsufficiency PMID2 Haploinsufficiency PMID3 Haploinsufficiency PMID4 Haploinsufficiency PMID5 Haploinsufficiency PMID6 Triplosensitivity Score Triplosensitivity Description Triplosensitivity PMID1 Triplosensitivity PMID2 Triplosensitivity PMID3 Triplosensitivity PMID4 Triplosensitivity PMID5 Triplosensitivity PMID6 Date Last Evaluated Haploinsufficiency Disease ID Triplosensitivity Disease ID +ISCA-46748 19p13.3 Critical Region 1 (CR1) 19p13.3 tbd 0 No evidence available 1 Little evidence for dosage pathogenicity 36196855 25853300 2023-10-10 MONDO:0100038 +ISCA-46747 22q11.2 recurrent region (distal type III, E/F-H) (includes SMARCB1) 22q11.22q11.23 chr22:23119415-24994433 3 Sufficient evidence for dosage pathogenicity 1 Little evidence for dosage pathogenicity 19193630 22140377 19006218 26247050 2023-01-25 +ISCA-46743 Xq25 region (includes STAG2) Xq25 chrX:123034319-123236519 3 Sufficient evidence for dosage pathogenicity 3 Sufficient evidence for dosage pathogenicity 23637084 24733578 26443594 25677961 31609727 2022-11-30 MONDO:0100038 +ISCA-46742 7p22.1 region (includes ACTB) 7p22.1 chr7:5536848-5799722 3 Sufficient evidence for dosage pathogenicity 27633570 29220674 32562408 1 Little evidence for dosage pathogenicity 26297194 21998864 22495914 25893121 25124455 27866048 2022-02-08 MONDO:0000508 MONDO:0100038 +ISCA-46741 9p24.3 Region (includes DMRT1) 9p24.3 chr9:1-1982069 2 Some evidence for dosage pathogenicity 20685758 22573722 23555275 32741963 Not yet evaluated Not yet evaluated 2023-11-10 MONDO:0002145 +ISCA-46739 Yq11.223 population region (DGV_Gold_Standard_June_2021_gssvL138428) Yq11.223 chrY:25853189-26146959 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46738 Yq11.223 population region (DGV_Gold_Standard_June_2021_gssvL138419) Yq11.223 chrY:24361866-24465171 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46737 Xq27.3 population region (DGV_Gold_Standard_June_2021_gssvL137799) Xq27.3 chrX:142601775-142800327 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46736 Xq21.1 population region (DGV_Gold_Standard_June_2021_gssvL136501) Xq21.1 chrX:76137628-76141022 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46735 Xp11.23 population region (DGV_Gold_Standard_June_2021_gssvL136075) Xp11.23 chrX:47880294-47952112 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46734 Xq28 population region (DGV_Gold_Standard_June_2021_gssvG41365) Xq28 chrX:153409846-153460630 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-03 +ISCA-46733 Xq24 population region (DGV_Gold_Standard_June_2021_gssvG41158) Xq24 chrX:120006512-120123897 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-03 +ISCA-46732 22q11.23 population region (DGV_Gold_Standard_June_2021_gssvG24415) 22q11.23 chr22:25703259-25785235 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-03 +ISCA-46731 22q11.21 population region (DGV_Gold_Standard_June_2021_gssvL77050) 22q11.21 chr22:21866876-21909287 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46730 22q11.21 population region (DGV_Gold_Standard_June_2021_gssvL77049) 22q11.21 chr22:21711480-21742055 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46729 22q11.21 population region (DGV_Gold_Standard_June_2021_gssvL77047) 22q11.21 chr22:21812558-21916568 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46728 22q11.21 population region (DGV_Gold_Standard_June_2021_gssvL76981) 22q11.21 chr22:20428070-20499197 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46727 22q11.22 population region (DGV_Gold_Standard_June_2021_gssvL77120) 22q11.22 chr22:23223448-23238992 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46726 22q11.23 population region (DGV_Gold_Standard_June_2021_gssvL77244) 22q11.23 chr22:24314289-24334833 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46725 22q11.23 population region (DGV_Gold_Standard_June_2021_gssvL77238) 22q11.23 chr22:24360812-24402386 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46724 12p11.2 population region (DGV_Gold_Standard_June_2021_gssvG23340) 21p11.2 chr21:10704853-10982352 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-03 +ISCA-46723 21q11.2 population region (DGV_Gold_Standard_June_2021_gssvL74506) 21q11.2 chr21:14957505-15202003 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46722 21q22.3 population region (DGV_Gold_Standard_June_2021_gssvL75982) 21q22.3 chr21:44969018-44974013 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46721 21q22.3 population region (DGV_Gold_Standard_June_2021_gssvL76000) 21q22.3 chr21:44970333-44971747 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46720 20p11.22 population region (DGV_Gold_Standard_June_2021_gssvL71898) 20p11.22 chr20:21486525-21496720 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46719 20q11.21 population region (DGV_Gold_Standard_June_2021_gssvL72187) 20q11.21 chr20:29509040-29536079 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46718 19p12 population region (DGV_Gold_Standard_June_2021_gssvL57428) 19p12 chr19:22087099-23141940 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46717 19q13.42 population region (DGV_Gold_Standard_June_2021_gssvG19479) 19q13.42 chr19:56280630-56289562 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46716 19p12 population region (DGV_Gold_Standard_June_2021_gssvL57316) 19p12 chr19:20594811-20725405 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46715 19p13.12 population region (DGV_Gold_Standard_June_2021_gssvL57062) 19p13.12 chr19:15727731-15787718 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46714 19q13.32 population region (DGV_Gold_Standard_June_2021_gssvL58890) 19q13.32 chr19:46622342-46628475 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46713 19q13.42 population region (DGV_Gold_Standard_June_2021_gssvL59370) 19q13.42 chr19:53939389-53976651 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46712 18q21.1 population region (DGV_Gold_Standard_June_2021_gssvG17872) 18q21.1 chr18:44542290-44558084 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46711 18p11.21 population region (DGV_Gold_Standard_June_2021_gssvG17388) 18p11.21 chr18:14432553-14565138 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46710 18q11.2 population region (DGV_Gold_Standard_June_2021_gssvL52661) 18q11.2 chr18:23747759-23751695 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46709 18p11.22 population region (DGV_Gold_Standard_June_2021_gssvL52196) 18p11.22 chr18:9784172-9793224 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46708 18p11.31 population region (DGV_Gold_Standard_June_2021_gssvL51911) 18p11.31 chr18:3568883-3571730 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46707 17q21.2 population region (DGV_Gold_Standard_June_2021_gssvG16538) 17q21.2 chr17:39531718-39539732 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46706 17q12 population region (DGV_Gold_Standard_June_2021_gssvG16427) 17q12 chr17:34502940-34524192 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46705 17p11.2 population region (DGV_Gold_Standard_June_2021_gssvG16095) 17p11.2 chr17:18359814-18376676 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46704 17p11.2 population region (DGV_Gold_Standard_June_2021_gssvG16067) 17p11.2 chr17:18361739-18423872 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46703 17p11.2 population region (DGV_Gold_Standard_June_2021_gssvG16017) 17p11.2 chr17:16711572-16724682 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46702 17p11.2 population region (DGV_Gold_Standard_June_2021_gssvG16012) 17p11.2 chr17:16660760-16707833 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46701 17p11.2 population region (DGV_Gold_Standard_June_2021_gssvL48488) 17p11.2 chr17:18359790-18376723 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46700 17p11.2 population region (DGV_Gold_Standard_June_2021_gssvL48476) 17p11.2 chr17:18418589-18465114 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46699 17p11.2 population region (DGV_Gold_Standard_June_2021_gssvL48375) 17p11.2 chr17:16711606-16724681 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46698 17q12 population region (DGV_Gold_Standard_June_2021_gssvL49126) 17q12 chr17:34509779-34551554 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46697 17q21.2 population region (DGV_Gold_Standard_June_2021_gssvL49379) 17q21.2 chr17:39383317-39396444 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46696 17q21.2 population region (DGV_Gold_Standard_June_2021_gssvL49386) 17q21.2 chr17:39429150-39433594 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46695 17q21.2 population region (DGV_Gold_Standard_June_2021_gssvL49384) 17q21.2 chr17:39422988-39430527 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46694 17q21.2 population region (DGV_Gold_Standard_June_2021_gssvL49383) 17q21.2 chr17:39384291-39392558 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46693 16q23.1 population region (DGV_Gold_Standard_June_2021_gssvG15270) 16q23.1 chr16:74387937-74459162 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46692 16q22.2 population region (DGV_Gold_Standard_June_2021_gssvG15245) 16q22.2 chr16:72088515-72116064 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46691 16p12.2 population region (DGV_Gold_Standard_June_2021_gssvG14372) 16p12.2 chr16:21512076-21595577 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46690 16p13.3 population region (DGV_Gold_Standard_June_2021_gssvL41949) 16p13.3 chr16:1289937-1295280 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46689 16p12.1 population region (DGV_Gold_Standard_June_2021_gssvL43366) 16p12.1 chr16:25066146-25137378 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46688 15q11.2 population region (DGV_Gold_Standard_June_2021_gssvG12359) 15q11.2 chr15:21145101-21164300 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46687 15q13.2 population region (DGV_Gold_Standard_June_2021_gssvG12633) 15q13.2 chr15:30488097-30796070 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46686 15q11.2 population region (DGV_Gold_Standard_June_2021_gssvG12224) 15q11.2 chr15:20388741-22207639 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46685 14q32.33 population region (DGV_Gold_Standard_June_2021_gssvG12150) 14q32.33 chr14:106805092-106814699 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46684 14q32.33 population region (DGV_Gold_Standard_June_2021_gssvG12133) 14q32.33 chr14:107147166-107164532 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46683 14q32.33 population region (DGV_Gold_Standard_June_2021_gssvG12117) 14q32.33 chr14:106826451-106850917 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46682 14q32.33 population region (DGV_Gold_Standard_June_2021_gssvG12097) 14q32.33 chr14:106118177-106145774 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46681 14q11.2 population region (DGV_Gold_Standard_June_2021_gssvG10899) 14q11.2 chr14:19462329-19469848 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46680 14q11.2 population region (DGV_Gold_Standard_June_2021_gssvG10827) 14q11.2 chr14:20335536-20423298 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46679 14q11.2 population region (DGV_Gold_Standard_June_2021_gssvG10817) 14q11.2 chr14:20190229-20426809 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46678 14q11.2 population region (DGV_Gold_Standard_June_2021_gssvL33520) 14q11.2 chr14:20190699-20425231 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46677 14q11.2 population region (DGV_Gold_Standard_June_2021_gssvL33589) 14q11.2 chr14:19462304-19469872 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46676 14q13.2 population region (DGV_Gold_Standard_June_2021_gssvL34350) 14q13.2 chr14:35605396-35615320 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46675 14q11.2 population region (DGV_Gold_Standard_June_2021_gssvG10810) 14q11.2 chr14:19596713-20418095 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46674 14q32.33 population region (DGV_Gold_Standard_June_2021_gssvL37239) 14q32.33 chr14:106483725-106508484 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46673 14q32.33 population region (DGV_Gold_Standard_June_2021_gssvL37313) 14q32.33 chr14:107172848-107183396 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46672 13q12.11 population region (DGV_Gold_Standard_June_2021_gssvG9718) 13q12.11 chr13:21534913-21541123 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46671 13q21.33 population region (DGV_Gold_Standard_June_2021_gssvL31119) 13q21.33 chr13:72476988-72489787 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46670 13q21.1 population region (DGV_Gold_Standard_June_2021_gssvL30434) 13q21.1 chr13:57768508-57786942 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46669 12p13.31 population region (DGV_Gold_Standard_June_2021_gssvG7850) 12p13.31 chr12:8361522-8391789 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46668 12p13.31 population region (DGV_Gold_Standard_June_2021_gssvG7792) 12p13.31 chr12:8558090-8596215 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46667 12p13.2 population region (DGV_Gold_Standard_June_2021_gssvL23179) 12p13.2 chr12:10581251-10597043 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46666 12q23.3 population region (DGV_Gold_Standard_June_2021_gssvL26928) 12q23.3 chr12:105369015-105374180 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46665 12p11.1 population region (DGV_Gold_Standard_June_2021_gssvL24290) 12p11.1 chr12:34355893-34361543 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46664 12p11.23 population region (DGV_Gold_Standard_June_2021_gssvL23860) 12p11.23 chr12:27647940-27654731 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46663 12p13.2 population region (DGV_Gold_Standard_June_2021_gssvL23231) 12p13.2 chr12:11224984-11240896 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46662 12p13.2 population region (DGV_Gold_Standard_June_2021_gssvL23228) 12p13.2 chr12:11227081-11251139 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46661 12p13.2 population region (DGV_Gold_Standard_June_2021_gssvL23223) 12p13.2 chr12:11191681-11217625 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46660 11q12.2 population region (DGV_Gold_Standard_June_2021_gssvG6800) 11q12.2 chr11:60966146-61020399 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46659 11p14.1 population region (DGV_Gold_Standard_June_2021_gssvG6305) 11p14.1 chr11:29007150-29012087 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46658 11p15.1 population region (DGV_Gold_Standard_June_2021_gssvG6192) 11p15.1 chr11:18940205-18963657 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46657 11p15.4 population region (DGV_Gold_Standard_June_2021_gssvG5957) 11p15.4 chr11:4255965-4278463 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46656 11p15.4 population region (DGV_Gold_Standard_June_2021_gssvG5919) 11p15.4 chr11:3239311-3360988 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46655 11p15.4 population region (DGV_Gold_Standard_June_2021_gssvL16784) 11p15.4 chr11:4968688-4980232 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46654 11p15.4 population region (DGV_Gold_Standard_June_2021_gssvL16737) 11p15.4 chr11:4255449-4278126 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46653 11p15.4 population region (DGV_Gold_Standard_June_2021_gssvL16732) 11p15.4 chr11:4264092-4309730 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46652 11p15.5 population region (DGV_Gold_Standard_June_2021_gssvL16511) 11p15.5 chr11:1915245-1937002 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46651 11p15.1 population region (DGV_Gold_Standard_June_2021_gssvL17400) 11p15.1 chr11:18941859-18964598 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46650 11p15.4 population region (DGV_Gold_Standard_June_2021_gssvL16961) 11p15.4 chr11:7809752-7834885 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46649 11p15.4 population region (DGV_Gold_Standard_June_2021_gssvL16881) 11p15.4 chr11:5873984-5883499 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46648 11q22.2 population region (DGV_Gold_Standard_June_2021_gssvL21098) 11q22.2 chr11:102751106-102752862 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46647 11q13.4 population region (DGV_Gold_Standard_June_2021_gssvL19865) 11q13.4 chr11:71850646-71889330 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46646 11q11 population region (DGV_Gold_Standard_June_2021_gssvL19045) 11q11 chr11:55434253-55443984 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46645 11q11 population region (DGV_Gold_Standard_June_2021_gssvL19042) 11q11 chr11:55445709-55457776 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46644 10q22.1 population region (DGV_Gold_Standard_June_2021_gssvL13249) 10q22.1 chr10:71282906-71291092 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46643 10q22.1 population region (DGV_Gold_Standard_June_2021_gssvL13247) 10q22.1 chr10:71280815-71291303 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46642 10q11.22 population region (DGV_Gold_Standard_June_2021_gssvL12112) 10q11.22 chr10:48902069-48986229 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46641 10q11.23 population region (DGV_Gold_Standard_June_2021_gssvL12109) 10q11.23 chr10:51861706-52000736 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46640 10q11.22 population region (DGV_Gold_Standard_June_2021_gssvL12105) 10q11.22 chr10:48664595-48872432 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46639 10q11.22 population region (DGV_Gold_Standard_June_2021_gssvG4512) 10q11.22 chr10:47531763-47597768 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46638 10p12.1 population region (DGV_Gold_Standard_June_2021_gssvL11273) 10p12.1 chr10:27638256-27642180 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46637 10p13 population region (DGV_Gold_Standard_June_2021_gssvL10668) 10p13 chr10:13259247-13260742 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46636 9q32 population region (DGV_Gold_Standard_June_2021_gssvG40321) 9q32 chr9:117078800-117098147 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46635 9p11.2 population region (DGV_Gold_Standard_June_2021_gssvG38779) 9p11.2 chr9:44283472-44840754 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46634 9p12 population region (DGV_Gold_Standard_June_2021_gssvL130637) 9p12 chr9:43589946-43694171 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46633 9p12 population region (DGV_Gold_Standard_June_2021_gssvL130619) 9p12 chr9:43584760-43755000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46632 9q31.1 population region (DGV_Gold_Standard_June_2021_gssvL132495) 9q31.1 chr9:107362715-107368622 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46631 8p23.1 population region (DGV_Gold_Standard_June_2021_gssvG36644) 8p23.1 chr8:7212582-7227421 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46630 8p23.1 population region (DGV_Gold_Standard_June_2021_gssvG36608) 8p23.1 chr8:6828736-6878156 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46629 8p23.1 population region (DGV_Gold_Standard_June_2021_gssvG36607) 8p23.1 chr8:7110945-7157807 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46628 7q36.1 population region (DGV_Gold_Standard_June_2021_gssvL119849) 7q36.1 chr7:150286146-150307909 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46627 7q35 population region (DGV_Gold_Standard_June_2021_gssvL119429) 7q35 chr7:143880615-144075919 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46626 7q35 population region (DGV_Gold_Standard_June_2021_gssvG35898) 7q35 chr7:143884211-143930465 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46625 7q22.1 population region (DGV_Gold_Standard_June_2021_gssvL117874) 7q22.1 chr7:101968967-102022209 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46624 7q34 population region (DGV_Gold_Standard_June_2021_gssvL119381) 7q34 chr7:142461276-142474923 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46623 7q34 population region (DGV_Gold_Standard_June_2021_gssvL119380) 7q34 chr7:142460176-142482236 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46622 7q34 population region (DGV_Gold_Standard_June_2021_gssvL119369) 7q34 chr7:142099063-142108894 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46621 7q34 population region (DGV_Gold_Standard_June_2021_gssvL119360) 7q34 chr7:142133273-142170344 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46620 7q11.23 population region (DGV_Gold_Standard_June_2021_gssvL116711) 7q11.23 chr7:74378312-74480711 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46619 7q11.21 population region (DGV_Gold_Standard_June_2021_gssvL116036) 7q11.21 chr7:62963166-62979392 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46618 7q11.21 population region (DGV_Gold_Standard_June_2021_gssvL115987) 7q11.21 chr7:62687315-62723648 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46617 7p11.2 population region (DGV_Gold_Standard_June_2021_gssvL115697) 7p11.2 chr7:57062764-57088685 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46616 7p14.1 population region (DGV_Gold_Standard_June_2021_gssvL115094) 7p14.1 chr7:38386563-38397743 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46615 7p22.1 population region (DGV_Gold_Standard_June_2021_gssvL113541) 7p22.1 chr7:6900773-6923243 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46614 6q13 population region (DGV_Gold_Standard_June_2021_gssvG32691) 6q13 chr6:74708884-74717014 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46613 6q13 population region (DGV_Gold_Standard_June_2021_gssvG32688) 6q13 chr6:74707825-74718498 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46612 6p25.3 population region (DGV_Gold_Standard_June_2021_gssvL104460) 6p25.3 chr6:83824-202184 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46611 6p21.32 population region (DGV_Gold_Standard_June_2021_gssvL106271) 6p21.32 chr6:32627550-32648423 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46610 6p21.32 population region (DGV_Gold_Standard_June_2021_gssvL106269) 6p21.32 chr6:32516836-32541693 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46609 6p21.32 population region (DGV_Gold_Standard_June_2021_gssvL106264) 6p21.32 chr6:32475856-32514239 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46608 6p22.1 population region (DGV_Gold_Standard_June_2021_gssvL105927) 6p22.1 chr6:29837200-29849273 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46607 6p22.1 population region (DGV_Gold_Standard_June_2021_gssvL105924) 6p22.1 chr6:29892560-29905834 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46605 5q13.2 population region (DGV_Gold_Standard_June_2021_gssvG30124) 5q13.2 chr5:69316084-69343660 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46604 5p15.33 population region (DGV_Gold_Standard_June_2021_gssvG29169) 5p15.33 chr5:814446-825367 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-05 +ISCA-46602 5q22.1 population region (DGV_Gold_Standard_June_2021_gssvL101506) 5q22.1 chr5:110905931-110911040 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46601 5q35.3 population region (DGV_Gold_Standard_June_2021_gssvL104429) 5q35.3 chr5:180591001-180596624 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-05 +ISCA-46600 5q35.3 population region (DGV_Gold_Standard_June_2021_gssvL104164) 5q35.3 chr5:178348352-178353194 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46599 5q31.3 population region (DGV_Gold_Standard_June_2021_gssvL102648) 5q31.3 chr5:140096767-140104053 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46598 4p11 population region (DGV_Gold_Standard_June_2021_gssvG27527) 4p11 chr4:49489242-49524812 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46597 4p16.1 population region (DGV_Gold_Standard_June_2021_gssvG27165) 4p16.1 chr4:9417997-9457368 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46596 4p16.1 population region (DGV_Gold_Standard_June_2021_gssvL88361) 4p16.1 chr4:9486907-9516088 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46595 4p11 population region (DGV_Gold_Standard_June_2021_gssvL90109) 4p11 chr4:49177189-49249875 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46594 4q13.2 population region (DGV_Gold_Standard_June_2021_gssvL90978) 4q13.2 chr4:70134832-70270391 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46593 4q13.3 population region (DGV_Gold_Standard_June_2021_gssvL91223) 4q13.3 chr4:75282628-75323181 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46592 3q29 population region (DGV_Gold_Standard_June_2021_gssvG26791) 3q29 chr3:195376588-195493533 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46591 3p12.3 population region (DGV_Gold_Standard_June_2021_gssvL82434) 3p12.3 chr3:75567345-75581692 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46590 3p12.3 population region (DGV_Gold_Standard_June_2021_gssvL82397) 3p12.3 chr3:75422907-75644624 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46589 3q29 population region (DGV_Gold_Standard_June_2021_gssvL86947) 3q29 chr3:195380278-195469564 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46588 3q25.31 population region (DGV_Gold_Standard_June_2021_gssvL85294) 3q25.31 chr3:155478166-155498646 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46587 3q11.2 population region (DGV_Gold_Standard_June_2021_gssvL83307) 3q11.2 chr3:97887492-97919334 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46586 3q11.2 population region (DGV_Gold_Standard_June_2021_gssvL83303) 3q11.2 chr3:97878295-97923426 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46585 2q37.3 population region (DGV_Gold_Standard_June_2021_gssvL70815) 2q37.3 chr2:242872862-243012181 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46584 2q21.1 population region (DGV_Gold_Standard_June_2021_gssvL66075) 2q21.1 chr2:130793882-130823249 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46583 2p11.2 population region (DGV_Gold_Standard_June_2021_gssvL64514) 2p11.2 chr2:90160287-90163570 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46582 2p11.2 population region (DGV_Gold_Standard_June_2021_gssvL64458) 2p11.2 chr2:90044437-90061011 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46581 2p11.2 population region (DGV_Gold_Standard_June_2021_gssvL64445) 2p11.2 chr2:90249376-90275932 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46580 2p11.2 population region (DGV_Gold_Standard_June_2021_gssvL64421) 2p11.2 chr2:89459244-89512939 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46579 2p11.2 population region (DGV_Gold_Standard_June_2021_gssvL64418) 2p11.2 chr2:90044551-90102805 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46578 2p11.2 population region (DGV_Gold_Standard_June_2021_gssvL64414) 2p11.2 chr2:90005834-90052218 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46577 1q44 population region (DGV_Gold_Standard_June_2021_gssvL8958) 1q44 chr1:248755655-248758478 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46576 1q44 population region (DGV_Gold_Standard_June_2021_gssvL8766) 1q44 chr1:248756880-248797809 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46575 1q41 population region (DGV_Gold_Standard_June_2021_gssvL7905) 1q41 chr1:222373208-222381462 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46574 1q24.2 population region (DGV_Gold_Standard_June_2021_gssvL5980) 1q24.2 chr1:168024558-168025732 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46573 1q23.3 population region (DGV_Gold_Standard_June_2021_gssvL5778) 1q23.3 chr1:161570323-161598180 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46572 1q21.3 population region (DGV_Gold_Standard_June_2021_gssvL5433) 1q21.3 chr1:152554926-152575348 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46571 1q21.2 population region (DGV_Gold_Standard_June_2021_gssvL5166) 1q21.2 chr1:149207851-149218151 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46570 1q21.2 population region (DGV_Gold_Standard_June_2021_gssvL5133) 1q21.2 chr1:149152064-149204067 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46569 1q21.2 population region (DGV_Gold_Standard_June_2021_gssvL5122) 1q21.2 chr1:147856152-147913592 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46568 1p31.3 population region (DGV_Gold_Standard_June_2021_gssvL3013) 1p31.3 chr1:64839912-64851868 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46567 1p31.3 population region (DGV_Gold_Standard_June_2021_gssvL2940) 1p31.3 chr1:62654661-62657211 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46566 1p36.12 population region (DGV_Gold_Standard_June_2021_gssvL1420) 1p36.12 chr1:22313123-22335712 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46565 1p36.13 population region (DGV_Gold_Standard_June_2021_gssvL1195) 1p36.13 chr1:17009445-17012777 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46564 1p36.21 population region (DGV_Gold_Standard_June_2021_gssvL1109) 1p36.21 chr1:16152667-16155517 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46563 1p36.21 population region (DGV_Gold_Standard_June_2021_gssvL1108) 1p36.21 chr1:16151690-16155602 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46562 1p36.21 population region (DGV_Gold_Standard_June_2021_gssvL905) 1p36.21 chr1:12899395-12924283 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46561 1p36.21 population region (DGV_Gold_Standard_June_2021_gssvL891) 1p36.21 chr1:12886641-12942069 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46560 1p36.21 population region (DGV_Gold_Standard_June_2021_gssvL889) 1p36.21 chr1:13692847-13774442 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46559 1q21.3 population region (DGV_Gold_Standard_June_2021_gssvG2465) 1q21.3 chr1:152761495-152773537 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46558 1p13.3 population region (DGV_Gold_Standard_June_2021_gssvG1423) 1p13.3 chr1:108917312-109000328 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46557 1p36.21 population region (DGV_Gold_Standard_June_2021_gssvG371) 1p36.21 chr1:12897609-12922238 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46556 1p36.33 population region (DGV_Gold_Standard_June_2021_gssvG23) 1p36.33 chr1:713039-756009 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46554 1p36.33 population region ((DGV_Gold_Standard_June_2021_gssvG23)) 1p36.33 chr1:713039-756009 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46553 3q24 Region (includes ZIC1) 3q24 chr3:136403035-148341113 3 Sufficient evidence for dosage pathogenicity 15338008 21204220 21471554 28503614 22067867 0 No evidence available 2021-07-19 MONDO:0000508 +ISCA-46552 Yq11.223 population region (gnomAD-SV_v2.1_DUP_Y_55057) Yq11.223 chrY:24024199-24070000 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-03 +ISCA-46551 Yq11.223 population region (gnomAD-SV_v2.1_DUP_Y_55049) Yq11.223 chrY:23656999-23713300 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-03 +ISCA-46550 Xq28 population region (gnomAD-SV_v2.1_DEL_X_190964) Xq28 chrX:155238299-155249500 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46549 Xq28 population region (gnomAD-SV_v2.1_DEL_X_190749) Xq28 chrX:153511999-153522000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46548 Xq28 population region (gnomAD-SV_v2.1_DEL_X_190688) Xq28 chrX:152240999-152251200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46547 Xq26.3 population region (gnomAD-SV_v2.1_DEL_X_189893) Xq26.3 chrX:134948399-134964600 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46546 Xq26.3 population region (gnomAD-SV_v2.1_DEL_X_189886) Xq26.3 chrX:134872199-134878900 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46545 Xq24 population region (gnomAD-SV_v2.1_DEL_X_189263) Xq24 chrX:120077116-120120000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46544 Xq24 population region (gnomAD-SV_v2.1_DEL_X_189262) Xq24 chrX:120063234-120090000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46543 Xp11.23 population region (gnomAD-SV_v2.1_DUP_X_53157) Xp11.23 chrX:49338999-49356900 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-03 +ISCA-46542 Xp11.23 population region (gnomAD-SV_v2.1_DUP_X_53155) Xp11.23 chrX:49328999-49343400 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-03 +ISCA-46541 Xp11.23 population region (gnomAD-SV_v2.1_DUP_X_53151) Xp11.23 chrX:49292999-49318650 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-03 +ISCA-46540 Xp11.23 population region (gnomAD-SV_v2.1_DUP_X_53149) Xp11.23 chrX:49197299-49208400 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-03 +ISCA-46539 Xp11.23 population region (gnomAD-SV_v2.1_DEL_X_186156) Xp11.23 chrX:49176299-49186050 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46538 22q13.1 population region (gnomAD-SV_v2.1_DEL_22_182715) 22q13.1 chr22:39358308-39388415 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46537 22q11.23 population region (gnomAD-SV_v2.1_DEL_22_181682) 22q11.23 chr22:24344399-24397000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46536 22q11.23 population region (gnomAD-SV_v2.1_DEL_22_181680) 22q11.23 chr22:24324299-24334200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46535 22q11.23 population region (gnomAD-SV_v2.1_DEL_22_181679) 22q11.23 chr22:24315999-24323000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46534 22q11.23 population region (gnomAD-SV_v2.1_DEL_22_181670) 22q11.23 chr22:24274143-24311297 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46533 22q11.21 population region (gnomAD-SV_v2.1_DEL_22_181532) 22q11.21 chr22:21562199-21569400 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46532 22q11.21 population region (gnomAD-SV_v2.1_DEL_22_181459) 22q11.21 chr22:20693999-20699000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46531 22q11.21 population region (gnomAD-SV_v2.1_DEL_22_181452) 22q11.21 chr22:20451599-20457600 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46530 22q11.21 population region (gnomAD-SV_v2.1_DEL_22_181446) 22q11.21 chr22:20366424-20371500 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46529 22q11.21 population region (gnomAD-SV_v2.1_DEL_22_181316) 22q11.21 chr22:18738599-18747000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46528 21q22.3 population region (gnomAD-SV_v2.1_DEL_21_181010) 21q22.3 chr21:47580927-47582908 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46527 21q11.2 population region (gnomAD-SV_v2.1_DEL_21_178683) 21q11.2 chr21:15012799-15034700 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46526 21q11.2 population region (gnomAD-SV_v2.1_DEL_21_178682) 21q11.2 chr21:14995199-15001200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46525 21q11.2 population region (gnomAD-SV_v2.1_DEL_21_178681) 21q11.2 chr21:14980399-14986100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46524 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173817) 19q13.42 chr19:55367999-55373100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46523 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173816) 19q13.42 chr19:55360499-55370000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46522 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173812) 19q13.42 chr19:55314899-55323600 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46521 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173811) 19q13.42 chr19:55301499-55324000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46520 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173809) 19q13.42 chr19:55292999-55298000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46519 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173807) 19q13.42 chr19:55285999-55293000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-03 +ISCA-46518 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173806) 19q13.42 chr19:55277999-55288000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46517 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173805) 19q13.42 chr19:55274849-55281600 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46516 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173803) 19q13.42 chr19:55256999-55289000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46515 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173802) 19q13.42 chr19:55251599-55257000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46514 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173801) 19q13.42 chr19:55250753-55267130 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46513 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173800) 19q13.42 chr19:55245599-55250700 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46512 19q13.42 population region (gnomAD-SV_v2.1_DEL_19_173749) 19q13.42 chr19:54800855-54807620 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46511 19q13.41 population region (gnomAD-SV_v2.1_DEL_19_173549) 19q13.41 chr19:53316224-53323725 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46510 19q13.41 population region (gnomAD-SV_v2.1_DEL_19_173445) 19q13.41 chr19:52134299-52149000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46509 19q13.41 population region (gnomAD-SV_v2.1_DEL_19_173443) 19q13.41 chr19:52127999-52139400 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46508 19q13.31 population region (gnomAD-SV_v2.1_DEL_19_172626) 19q13.31 chr19:43700999-43716000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46507 19q13.31 population region (gnomAD-SV_v2.1_DEL_19_172625) 19q13.31 chr19:43700966-43764809 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46506 19q13.12 population region (gnomAD-SV_v2.1_DEL_19_172006) 19q13.12 chr19:35850999-35863275 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46505 19p13.2 population region (gnomAD-SV_v2.1_DUP_19_46817) 19p13.2 chr19:7019174-7060500 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46504 17q21.31 population region (gnomAD-SV_v2.1_DEL_17_160670) 17q21.31 chr17:44637999-44653000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46503 17q21.31 population region (gnomAD-SV_v2.1_DEL_17_160664) 17q21.31 chr17:44403899-44409900 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46502 17q21.31 population region (gnomAD-SV_v2.1_DEL_17_160663) 17q21.31 chr17:44401199-44418450 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46501 17q21.31 population region (gnomAD-SV_v2.1_DEL_17_160662) 17q21.31 chr17:44399099-44405700 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46500 17q21.31 population region (gnomAD-SV_v2.1_DEL_17_160659) 17q21.31 chr17:44381699-44387000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46499 17q21.31 population region (gnomAD-SV_v2.1_DEL_17_160658) 17q21.31 chr17:44368999-44380000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46498 17q21.2 population region (gnomAD-SV_v2.1_DUP_17_44064) 17q21.2 chr17:39531966-39539289 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46497 17q21.2 population region (gnomAD-SV_v2.1_DEL_17_160290) 17q21.2 chr17:39421793-39432145 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46496 17q21.2 population region (gnomAD-SV_v2.1_DEL_17_160287) 17q21.2 chr17:39383999-39395000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46495 17p11.2 population region (gnomAD-SV_v2.1_DEL_17_159095) 17p11.2 chr17:19014999-19054000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46494 17p11.2 population region (gnomAD-SV_v2.1_DEL_17_159047) 17p11.2 chr17:18329998-18465150 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46493 16q22.1 population region (gnomAD-SV_v2.1_DUP_16_42449) 16q22.1 chr16:70094243-70242956 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46492 16p11.2 population region (gnomAD-SV_v2.1_DEL_16_153860) 16p11.2 chr16:32655999-32802000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46491 16p11.2 population region (gnomAD-SV_v2.1_DUP_16_42022) 16p11.2 chr16:32019999-32096000 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-04 +ISCA-46490 16p11.2 population region (gnomAD-SV_v2.1_DEL_16_153573) 16p11.2 chr16:28764999-28772000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46489 16p11.2 population region (gnomAD-SV_v2.1_DEL_16_153568) 16p11.2 chr16:28715099-28771000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-04 +ISCA-46488 16p12.3 population region (gnomAD-SV_v2.1_DEL_16_152900) 16p12.3 chr16:18414999-18421000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46487 16p13.11 population region (gnomAD-SV_v2.1_DEL_16_152730) 16p13.11 chr16:16329599-16364350 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-23 +ISCA-46485 16p13.12 population region (gnomAD-SV_v2.1_DEL_16_152600) 16p13.12 chr16:14782999-14853150 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46484 16p13.12 population region (gnomAD-SV_v2.1_DEL_16_152599) 16p13.12 chr16:14782199-14805000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46483 16p13.3 population region (gnomAD-SV_v2.1_DEL_16_151010) 16p13.3 chr16:59999-65000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46482 15q14 population region (gnomAD-SV_v2.1_DEL_15_146739) 15q14 chr15:34726357-34872885 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46481 15q14 population region (gnomAD-SV_v2.1_DEL_15_146738) 15q14 chr15:34710126-34856557 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46480 15q13.3 population region (gnomAD-SV_v2.1_DEL_15_146627) 15q13.3 chr15:32886199-32898000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46479 15q13.3 population region (gnomAD-SV_v2.1_DEL_15_146625) 15q13.3 chr15:32864999-32898000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46478 15q13.3 population region (gnomAD-SV_v2.1_DEL_15_146614) 15q13.3 chr15:32774999-32780000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46477 15q13.3 population region (gnomAD-SV_v2.1_DEL_15_146612) 15q13.3 chr15:32743999-32755100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46476 15q13.3 population region (gnomAD-SV_v2.1_DEL_15_146609) 15q13.3 chr15:32692999-32698000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46475 15q13.3 population region (gnomAD-SV_v2.1_DUP_15_39790) 15q13.3 chr15:32690774-32734250 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-09 +ISCA-46474 15q13.2 population region (gnomAD-SV_v2.1_DEL_15_146467) 15q13.2 chr15:30847949-30883100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46473 15q13.2 population region (gnomAD-SV_v2.1_DEL_15_146464) 15q13.2 chr15:30825199-30853100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46472 15q13.2 population region (gnomAD-SV_v2.1_DEL_15_146452) 15q13.2 chr15:30692999-30725200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46471 15q13.2 population region (gnomAD-SV_v2.1_DEL_15_146453) 15q13.2 chr15:30432998-30883100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46470 15q13.2 population region (gnomAD-SV_v2.1_DEL_15_146428) 15q13.2 chr15:30381948-30438500 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46469 15q11.2 population region (gnomAD-SV_v2.1_DEL_15_145837) 15q11.2 chr15:21042049-21056300 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46468 15q11.2 population region (gnomAD-SV_v2.1_DEL_15_145826) 15q11.2 chr15:20729174-20745525 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46467 14q11.2 population region (gnomAD-SV_v2.1_DEL_14_140616) 14q11.2 chr14:24467999-24474000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46466 12q12 population region (gnomAD-SV_v2.1_DEL_12_127735) 12q12 chr12:40874766-40876424 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46465 12p11.23 population region (gnomAD-SV_v2.1_DEL_12_126677) 12p11.23 chr12:27648141-27655163 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46464 12p13.2 population region (gnomAD-SV_v2.1_DEL_12_125610) 12p13.2 chr12:11225999-11250600 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46463 12p13.2 population region (gnomAD-SV_v2.1_DEL_12_125568) 12p13.2 chr12:10581599-10587675 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46462 12p13.2 population region (gnomAD-SV_v2.1_DEL_12_125567) 12p13.2 chr12:10581544-10597003 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46461 12p13.31 population region (gnomAD-SV_v2.1_DUP_12_33971) 12p13.31 chr12:8361449-8390896 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-09 +ISCA-46460 11q14.3 population region (gnomAD-SV_v2.1_DEL_11_121860) 11q14.3 chr11:89762999-89783400 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46459 11q14.3 population region (gnomAD-SV_v2.1_DUP_11_33042) 11q14.3 chr11:89520077-89657031 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-09 +ISCA-46458 11q11 population region (gnomAD-SV_v2.1_DEL_11_119564) 11q11 chr11:55364275-55444015 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46457 11q11 population region (gnomAD-SV_v2.1_DEL_11_119505) 11q11 chr11:55031602-55038540 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-09 +ISCA-46456 11p15.4 population region (gnomAD-SV_v2.1_DEL_11_116241) 11p15.4 chr11:7811175-7833378 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46455 11p15.4 population region (gnomAD-SV_v2.1_DEL_11_116124) 11p15.4 chr11:5873988-5883493 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46454 11p15.4 population region (gnomAD-SV_v2.1_DEL_11_116046) 11p15.4 chr11:4967746-4976658 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46453 10q22.3 population region (gnomAD-SV_v2.1_DEL_10_112166) 10q22.3 chr10:81604499-81610800 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46452 10q11.23 population region (gnomAD-SV_v2.1_DEL_10_110230) 10q11.23 chr10:51973199-51981300 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46451 10q11.23 population region (gnomAD-SV_v2.1_DEL_10_110229) 10q11.23 chr10:51967199-51974400 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46450 10q11.23 population region (gnomAD-SV_v2.1_DEL_10_110225) 10q11.23 chr10:51861999-51894650 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46449 10q11.23 population region (gnomAD-SV_v2.1_DEL_10_110224) 10q11.23 chr10:51858299-51864600 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46448 10q11.23 population region (gnomAD-SV_v2.1_DEL_10_110223) 10q11.23 chr10:51851849-51857400 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46447 10q11.23 population region (gnomAD-SV_v2.1_DEL_10_110222) 10q11.23 chr10:51845699-51850800 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46446 10q11.23 population region (gnomAD-SV_v2.1_DEL_10_110221) 10q11.23 chr10:51839699-51845100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46445 10q11.23 population region (gnomAD-SV_v2.1_DEL_10_110193) 10q11.23 chr10:51219499-51231000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46444 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110072) 10q11.22 chr10:48806124-48812000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46443 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110044) 10q11.22 chr10:48251999-48258000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46442 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110043) 10q11.22 chr10:48239999-48247800 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46441 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110040) 10q11.22 chr10:48197999-48248000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46440 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110031) 10q11.22 chr10:48020299-48039225 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46439 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110022) 10q11.22 chr10:47932799-47938200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46438 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110021) 10q11.22 chr10:47927849-47935000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46437 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110019) 10q11.22 chr10:47896499-47919300 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46436 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110016) 10q11.22 chr10:47748899-47754600 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46435 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110001) 10q11.22 chr10:47211299-47216400 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46434 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_110000) 10q11.22 chr10:47191199-47201400 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46433 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_109999) 10q11.22 chr10:47177699-47182800 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46432 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_109998) 10q11.22 chr10:47171999-47177000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46431 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_109958) 10q11.22 chr10:46338599-46375000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46430 10q11.22 population region (gnomAD-SV_v2.1_DEL_10_109954) 10q11.22 chr10:46310649-46325800 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46429 10p12.33 population region (gnomAD-SV_v2.1_DEL_10_108289) 10p12.33 chr10:18126899-18135000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46428 10p12.33 population region (gnomAD-SV_v2.1_DEL_10_108288) 10p12.33 chr10:18117799-18130100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46427 10p12.33 population region (gnomAD-SV_v2.1_DEL_10_108283) 10p12.33 chr10:17879999-17893800 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46426 10p12.33 population region (gnomAD-SV_v2.1_DEL_10_108282) 10p12.33 chr10:17867999-17880000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46425 9q34.3 population region (gnomAD-SV_v2.1_DEL_9_106704) 9q34.3 chr9:138936849-138944500 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46424 9q31.2 population region (gnomAD-SV_v2.1_DEL_9_104809) 9q31.2 chr9:110537534-110540595 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46423 9q21.11 population region (gnomAD-SV_v2.1_DUP_9_27462) 9q21.11 chr9:70631499-70655275 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-17 +ISCA-46422 9q21.11 population region (gnomAD-SV_v2.1_DUP_9_27460) 9q21.11 chr9:70557057-70693525 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-10 +ISCA-46421 9q21.11 population region (gnomAD-SV_v2.1_DEL_9_102461) 9q21.11 chr9:69418924-69435100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46420 9q21.11 population region (gnomAD-SV_v2.1_DEL_9_102460) 9q21.11 chr9:69398749-69405200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46419 9q21.11 population region (gnomAD-SV_v2.1_DEL_9_102459) 9q21.11 chr9:69375499-69388225 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46418 9q13 population region (gnomAD-SV_v2.1_DEL_9_102391) 9q13 chr9:67954499-67986500 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-10 +ISCA-46417 9q12 population region (gnomAD-SV_v2.1_DEL_9_102303) 9q12 chr9:65496999-65509000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46416 9p11.1 population region (gnomAD-SV_v2.1_DEL_9_102297) 9p11.1 chr9:47307099-47317679 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46415 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102296) 9p11.2 chr9:47298999-47304000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46414 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102294) 9p11.2 chr9:47281174-47300125 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46413 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102236) 9p11.2 chr9:46366999-46389000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46412 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102187) 9p11.2 chr9:45728849-45746725 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46411 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102099) 9p11.2 chr9:44399899-44405000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46410 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102097) 9p11.2 chr9:44391999-44411000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46409 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102096) 9p11.2 chr9:44388999-44470300 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46408 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102085) 9p11.2 chr9:44313499-44331000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46407 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102049) 9p11.2 chr9:43915599-43920850 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46406 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102048) 9p11.2 chr9:43902774-43914325 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46405 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102047) 9p11.2 chr9:43870599-43899100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46404 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102046) 9p11.2 chr9:43870599-43876000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46403 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102043) 9p11.2 chr9:43800749-43849800 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46402 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102042) 9p11.2 chr9:43795899-43804300 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46401 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102036) 9p11.2 chr9:43733799-43739000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46400 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102035) 9p11.2 chr9:43723999-43739000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46399 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102032) 9p11.2 chr9:43708999-43728000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46398 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102027) 9p11.2 chr9:43628499-43647400 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46397 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102025) 9p11.2 chr9:43623999-43631000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46396 9p11.2 population region (gnomAD-SV_v2.1_DEL_9_102024) 9p11.2 chr9:43622999-43708000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46395 9p12 population region (gnomAD-SV_v2.1_DEL_9_101967) 9p12 chr9:42363999-42374800 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46394 9p12 population region (gnomAD-SV_v2.1_DEL_9_101925) 9p12 chr9:41499999-41507000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46393 9p12 population region (gnomAD-SV_v2.1_DEL_9_101915) 9p12 chr9:41322999-41329000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46392 9p13.1 population region (gnomAD-SV_v2.1_DEL_9_101840) 9p13.1 chr9:40024899-40031800 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46391 9p24.3 population region (gnomAD-SV_v2.1_DUP_9_26178) 9p24.3 chr9:111999-126000 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-11 +ISCA-46390 8q24.3 population region (gnomAD-SV_v2.1_DEL_8_98285) 8q24.3 chr8:145479999-145502750 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46389 8q24.3 population region (gnomAD-SV_v2.1_DEL_8_98283) 8q24.3 chr8:145312849-145332400 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46388 8p23.1 population region (gnomAD-SV_v2.1_DEL_8_89725) 8p23.1 chr8:12291199-12311050 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46387 8p23.1 population region (gnomAD-SV_v2.1_DUP_8_23819) 8p23.1 chr8:12251799-12297400 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-11 +ISCA-46386 8p23.1 population region (gnomAD-SV_v2.1_DEL_8_89706) 8p23.1 chr8:11961999-11968000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46385 8p23.1 population region (gnomAD-SV_v2.1_DEL_8_89703) 8p23.1 chr8:11903999-11926000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46384 8p23.1 population region (gnomAD-SV_v2.1_DEL_8_89357) 8p23.1 chr8:7806249-7812100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46383 8p23.1 population region (gnomAD-SV_v2.1_DEL_8_89356) 8p23.1 chr8:7798999-7824100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46382 8p23.1 population region (gnomAD-SV_v2.1_DEL_8_89355) 8p23.1 chr8:7744999-7754100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46381 8p23.1 population region (gnomAD-SV_v2.1_DUP_8_23708) 8p23.1 chr8:7736999-7743100 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-17 +ISCA-46380 8p23.1 population region (gnomAD-SV_v2.1_DEL_8_89353) 8p23.1 chr8:7736499-7764500 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46379 8p23.3 population region (gnomAD-SV_v2.1_DEL_8_88408) 8p23.3 chr8:116099-129200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46378 8p23.3 population region (gnomAD-SV_v2.1_DEL_8_88399) 8p23.3 chr8:25899-33100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46377 7q35 population region (gnomAD-SV_v2.1_DEL_7_87112) 7q35 chr7:143408999-143417500 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46376 7q34 population region (gnomAD-SV_v2.1_DEL_7_87016) 7q34 chr7:141765424-141794499 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46375 7q34 population region (gnomAD-SV_v2.1_DEL_7_87015) 7q34 chr7:141754993-141780979 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-11 +ISCA-46374 7q22.1 population region (gnomAD-SV_v2.1_DEL_7_84412) 7q22.1 chr7:102300999-102331000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46373 7q22.1 population region (gnomAD-SV_v2.1_DEL_7_84190) 7q22.1 chr7:99461390-99463562 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46372 7q11.23 population region (gnomAD-SV_v2.1_DEL_7_82638) 7q11.23 chr7:74468999-74476300 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46371 7q11.23 population region (gnomAD-SV_v2.1_DEL_7_82637) 7q11.23 chr7:74452999-74459200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46370 7q11.23 population region (gnomAD-SV_v2.1_DEL_7_82636) 7q11.23 chr7:74420999-74428000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46369 7q11.23 population region (gnomAD-SV_v2.1_DEL_7_82621) 7q11.23 chr7:74223499-74230000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46368 7q11.21 population region (gnomAD-SV_v2.1_DEL_7_81890) 7q11.21 chr7:65110999-65144000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46367 7p22.1 population region (gnomAD-SV_v2.1_DEL_7_77893) 7p22.1 chr7:6818999-6827200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46366 7p22.1 population region (gnomAD-SV_v2.1_DEL_7_77769) 7p22.1 chr7:5976999-5982000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46365 7p22.1 population region (gnomAD-SV_v2.1_DEL_7_77765) 7p22.1 chr7:5940999-5953000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46364 5q35.3 population region (gnomAD-SV_v2.1_DEL_5_65880) 5q35.3 chr5:180787999-180857000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46363 5q35.3 population region (gnomAD-SV_v2.1_DEL_5_65831) 5q35.3 chr5:180375131-180430626 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46362 5q31.3 population region (gnomAD-SV_v2.1_DEL_5_63328) 5q31.3 chr5:140222136-140238931 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46361 5q13.2 population region (gnomAD-SV_v2.1_DEL_5_58900) 5q13.2 chr5:70326999-70335700 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46360 5q13.2 population region (gnomAD-SV_v2.1_DUP_5_15442) 5q13.2 chr5:70324499-70404000 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-12 +ISCA-46359 5q13.2 population region (gnomAD-SV_v2.1_DEL_5_58897) 5q13.2 chr5:70312999-70365100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46358 5q13.2 population region (gnomAD-SV_v2.1_DUP_5_15350) 5q13.2 chr5:69305399-69369100 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-12 +ISCA-46357 4q13.3 population region (gnomAD-SV_v2.1_DEL_4_46753) 4q13.3 chr4:75483999-75493000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46356 4q13.3 population region (gnomAD-SV_v2.1_DEL_4_46744) 4q13.3 chr4:75315999-75323000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46355 4q13.2 population region (gnomAD-SV_v2.1_DEL_4_46404) 4q13.2 chr4:70152039-70261334 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46354 4q13.2 population region (gnomAD-SV_v2.1_DEL_4_46401) 4q13.2 chr4:70138063-70247165 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46353 4q13.2 population region (gnomAD-SV_v2.1_DEL_4_46399) 4q13.2 chr4:70126481-70235359 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46352 4q13.2 population region (gnomAD-SV_v2.1_DEL_4_46398) 4q13.2 chr4:70123999-70171300 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46351 4q13.2 population region (gnomAD-SV_v2.1_DEL_4_46396) 4q13.2 chr4:70123650-70232337 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46350 3p12.3 population region (gnomAD-SV_v2.1_DEL_3_33722) 3p12.3 chr3:75767999-75796000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46349 2q21.2 population region (gnomAD-SV_v2.1_DUP_2_6167) 2q21.2 chr2:132853576-133213563 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46348 2q21.2 population region (gnomAD-SV_v2.1_DEL_2_22275) 2q21.2 chr2:132519999-132529000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46347 2q21.1 population region (gnomAD-SV_v2.1_DEL_2_22163) 2q21.1 chr2:131412799-131430000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46346 2q21.1 population region (gnomAD-SV_v2.1_DEL_2_22156) 2q21.1 chr2:131248899-131254600 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46345 2q21.1 population region (gnomAD-SV_v2.1_DEL_2_22155) 2q21.1 chr2:131236999-131242000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46344 2q21.1 population region (gnomAD-SV_v2.1_DEL_2_22135) 2q21.1 chr2:130954938-130957387 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46343 2q21.1 population region (gnomAD-SV_v2.1_DEL_2_22133) 2q21.1 chr2:130953999-130959000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46342 2p11.2 population region (gnomAD-SV_v2.1_DEL_2_19888) 2p11.2 chr2:87242199-87253600 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46341 1q44 population region (gnomAD-SV_v2.1_DEL_1_13898) 1q44 chr1:248806699-248819725 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46340 1q44 population region (gnomAD-SV_v2.1_DEL_1_13890) 1q44 chr1:248737999-248744000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46339 1q44 population region (gnomAD-SV_v2.1_DEL_1_13889) 1q44 chr1:248730999-248798200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46338 1q44 population region (gnomAD-SV_v2.1_DEL_1_13888) 1q44 chr1:248728999-248743000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46337 1q44 population region (gnomAD-SV_v2.1_DEL_1_13885) 1q44 chr1:248712454-248757403 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46336 1q44 population region (gnomAD-SV_v2.1_DUP_1_3816) 1q44 chr1:248619999-248647000 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46335 1q32.2 population region (gnomAD-SV_v2.1_DEL_1_11282) 1q32.2 chr1:207708749-207718050 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-16 +ISCA-46334 1q25.2 population region (gnomAD-SV_v2.1_DEL_1_9549) 1q25.2 chr1:179455597-179458296 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46333 1q23.3 population region (gnomAD-SV_v2.1_DEL_1_8646) 1q23.3 chr1:161529258-161610923 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46332 1q21.3 population region (gnomAD-SV_v2.1_DEL_1_8087) 1q21.3 chr1:152760519-152771091 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46331 1q21.3 population region (gnomAD-SV_v2.1_DEL_1_8075) 1q21.3 chr1:152555541-152587740 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46330 1q21.2 population region (gnomAD-SV_v2.1_DEL_1_7863) 1q21.2 chr1:149396649-149406100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46329 1q21.2 population region (gnomAD-SV_v2.1_DEL_1_7859) 1q21.2 chr1:149368999-149433200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46328 1q21.2 population region (gnomAD-SV_v2.1_DEL_1_7798) 1q21.2 chr1:147944999-147955500 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46327 1q21.2 population region (gnomAD-SV_v2.1_DEL_1_7795) 1q21.2 chr1:147931899-147982900 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46326 1q21.2 population region (gnomAD-SV_v2.1_DEL_1_7781) 1q21.2 chr1:147559999-147630500 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46325 1q21.2 population region (gnomAD-SV_v2.1_DEL_1_7778) 1q21.2 chr1:147433599-147455000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46324 1q21.1 population region (gnomAD-SV_v2.1_DEL_1_7699) 1q21.1 chr1:146025999-146089000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46323 1p13.3 population region (gnomAD-SV_v2.1_DEL_1_7022) 1p13.3 chr1:110230194-110254581 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46322 1p13.3 population region (gnomAD-SV_v2.1_DEL_1_6959) 1p13.3 chr1:108923349-108996100 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46321 1p21.1 population region (gnomAD-SV_v2.1_DUP_1_1884) 1p21.1 chr1:104190999-104303200 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46320 1p36.11 population region (gnomAD-SV_v2.1_DEL_1_1945) 1p36.11 chr1:25654999-25661350 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46319 1p36.11 population region (gnomAD-SV_v2.1_DEL_1_1944) 1p36.11 chr1:25644399-25649500 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46318 1p36.11 population region (gnomAD-SV_v2.1_DEL_1_1943) 1p36.11 chr1:25639499-25650000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46317 1p36.11 population region (gnomAD-SV_v2.1_DEL_1_1941) 1p36.11 chr1:25630899-25636000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46316 1p36.11 population region (gnomAD-SV_v2.1_DEL_1_1939) 1p36.11 chr1:25613999-25621000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46315 1p36.11 population region (gnomAD-SV_v2.1_DEL_1_1938) 1p36.11 chr1:25593699-25610200 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46314 1p36.11 population region (gnomAD-SV_v2.1_DEL_1_1937) 1p36.11 chr1:25592799-25651000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-17 +ISCA-46313 1p36.11 population region (gnomAD-SV_v2.1_DEL_1_1834) 1p36.11 chr1:24283999-24291000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-12 +ISCA-46312 1p36.21 population region (gnomAD-SV_v2.1_DEL_1_1100) 1p36.21 chr1:13043099-13052800 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46311 1p36.21 population region (gnomAD-SV_v2.1_DEL_1_1094) 1p36.21 chr1:12989199-12998900 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46310 1p36.21 population region (gnomAD-SV_v2.1_DEL_1_1089) 1p36.21 chr1:12949999-12966000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46309 1p36.21 population region (gnomAD-SV_v2.1_DEL_1_1085) 1p36.21 chr1:12896424-12930275 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46308 1p36.21 population region (gnomAD-SV_v2.1_DUP_1_507) 1p36.21 chr1:12894999-12940000 0 No evidence available 40 Dosage sensitivity unlikely 2021-08-06 +ISCA-46307 1p36.33 population region (gnomAD-SV_v2.1_DEL_1_195) 1p36.33 chr1:1640999-1647000 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46306 1p36.33 population region (gnomAD-SV_v2.1_DEL_1_11) 1p36.33 chr1:363999-401750 40 Dosage sensitivity unlikely 0 No evidence available 2021-08-06 +ISCA-46304 Xq28 region (includes MECP2) Xq28 chrX:153273980-153375749 0 No evidence available 3 Sufficient evidence for dosage pathogenicity 32043567 29618507 22679399 29141583 2021-02-22 MONDO:0010283 +ISCA-46303 SOX9 upstream enhancer region 17q24.3 chr17:67892996-69792434 3 Sufficient evidence for dosage pathogenicity 19234473 26663529 24934569 1 Little evidence for dosage pathogenicity 32583964 19639023 2021-06-07 MONDO:0007134 MONDO:0009869 +ISCA-46302 Xp21.2 region (includes NR0B1) Xp21.2 chrX:30195000-30355000 0 No evidence available 3 Sufficient evidence for dosage pathogenicity 22518125 17504899 20685758 2020-07-22 MONDO:0010226 +ISCA-46300 15q24 recurrent region (LCR C-LCR D) (includes SIN3A) 15q24 chr15:75631787-75972909 3 Sufficient evidence for dosage pathogenicity 27399968 22180641 0 No evidence available 2020-01-13 MONDO:0013256 +ISCA-46299 Xp11.22 region (includes HUWE1) Xp11.22 chrX:53363456-53793054 0 No evidence available 3 Sufficient evidence for dosage pathogenicity 22840365 20655035 26692240 2018-11-19 MONDO:0020119 +ISCA-46298 13q12.12 recurrent region (includes SACS, SGCG) 13q12.12 chr13:23544582-24881361 0 No evidence available 30767844 40 Dosage sensitivity unlikely 2021-04-26 +ISCA-46297 16p12.2 recurrent region (distal)(includes OTOA) 16p12.2 chr16:21570113-21740423 30 Gene associated with autosomal recessive phenotype 40 Dosage sensitivity unlikely 2019-11-03 MONDO:0011762 +ISCA-46296 15q24 recurrent region (LCR A-LCR C) 15q24.1-q24.2 chr15:72963715-75508312 3 Sufficient evidence for dosage pathogenicity 22180641 19921647 1 Little evidence for dosage pathogenicity 19557438 20860070 2020-01-03 +ISCA-46295 15q13.3 recurrent region (D-CHRNA7 to BP5) (includes CHRNA7, OTUD7A) 15q13.3 chr15:32019621-32445405 3 Sufficient evidence for dosage pathogenicity 19898479 20236110 22775350 40 Dosage sensitivity unlikely 26968334 22420048 2018-05-10 MONDO:0100038 +ISCA-46294 22q11.2 recurrent region (distal type III, F-G) (includes SMARCB1) 22q11.23 chr22:23831202-24632821 3 Sufficient evidence for dosage pathogenicity 21208904 0 No evidence available 2022-09-30 +ISCA-46292 22q11.2 recurrent region (distal type III, D-G/H) (includes SMARCB1) 22q11.21-q11.23 chr22:21917117-24994433 3 Sufficient evidence for dosage pathogenicity 21671380 21187175 17541642 0 No evidence available 2023-03-27 MONDO:0012252 +ISCA-46291 7q11.23 recurrent distal region (includes HIP1, YWHAG) 7q11.23 chr7:75158048-76063176 2 Some evidence for dosage pathogenicity 21109226 35481155 16971481 1 Little evidence for dosage pathogenicity 21109226 27867344 2023-04-20 +ISCA-46290 Xp11.22p11.23 recurrent region (includes SHROOM4) Xp11.22-p11.23 chrX:48306152-52103258 0 No evidence available 3 Sufficient evidence for dosage pathogenicity 19716111 21418194 25425167 2017-12-14 MONDO:0010428 +ISCA-46288 2q21.1 recurrent region (includes ARHGEF4, GPR148) 2q21.1 chr2:131477509-131929693 1 Little evidence for dosage pathogenicity 22543972 24591035 25661985 0 No evidence available 22543972 2019-09-30 +ISCA-46287 2p24.3 MYCN-DDX1 duplication region 2p24.3 chr2:15708677-16185337 2 Some evidence for dosage pathogenicity 27794475 24161495 23401364 2017-08-07 MONDO:0005072 +ISCA-46285 15q13 recurrent region (BP3-BP4) (includes APBA2) 15q13.1-q13.2 chr15:29156959-30368990 0 No evidence available 21248749 19372089 18278044 0 No evidence available 2020-03-09 +ISCA-37516 22q11.2 recurrent region (central, B/C-D) (includes CRKL) 22q11.21 chr22:20731986-21465672 2 Some evidence for dosage pathogenicity 25123976 29090080 26278718 22893440 28121514 0 No evidence available 30614210 29090080 18445048 18414210 19490635 22796526 2022-08-29 +ISCA-37514 15q25.2q25.3 recurrent region (distal, LCR C-LCR D) 15q25.2-q25.3 chr15:85139652-85713001 1 Little evidence for dosage pathogenicity 23239641 0 No evidence available 2020-06-26 +ISCA-37501 17q23.1q23.2 recurrent region (includes TBX2, TBX4) 17q23.1-q23.2 chr17:58113002-60275809 3 Sufficient evidence for dosage pathogenicity 20206336 22052739 2 Some evidence for dosage pathogenicity 20598276 24592505 2018-11-19 MONDO:0013238 +ISCA-37500 15q25.2 recurrent region (proximal LCR B-LCR C) 15q25.2 chr15:83213988-84714733 3 Sufficient evidence for dosage pathogenicity 24352913 23166063 17847001 0 No evidence available 2016-10-13 MONDO:0013672 +ISCA-37498 11q13.2q13.4 recurrent region (includes SHANK2, FGFs) 11q13.2-q13.4 chr11:67763646-71236931 2 Some evidence for dosage pathogenicity 21373257 28211979 0 No evidence available 2022-09-27 +ISCA-37497 10q11.2 recurrent region (LCR C-LCR D) 10q11.22-q11.23 chr10:49389703-51053583 1 Little evidence for dosage pathogenicity 21948486 20466309 17531565 1 Little evidence for dosage pathogenicity 21948486 24669257 28846756 34207052 2022-10-12 +ISCA-37496 2q13 recurrent region (includes BCL2L11) 2q13 chr2:111392193-113104742 2 Some evidence for dosage pathogenicity 26227573 26236398 21255006 2 Some evidence for dosage pathogenicity 26227573 24807792 21255006 2018-06-22 +ISCA-37495 2q11.2 recurrent region (includes ARID5A, TMEM127) 2q11.2 chr2:96739012-97671429 3 Sufficient evidence for dosage pathogenicity 26227573 1 Little evidence for dosage pathogenicity 26227573 2022-02-21 +ISCA-37494 Xq28 recurrent region (int22h1/int22h2-flanked) (includes RAB39B) Xq28 chrX:154118603-154564401 3 Sufficient evidence for dosage pathogenicity 25927380 21984752 3 Sufficient evidence for dosage pathogenicity 25927380 21984752 24357492 2018-08-30 MONDO:0010436 +ISCA-37493 1q43q44 terminal region (includes AKT3) 1q43-q44 chr1:243287730-245318287 3 Sufficient evidence for dosage pathogenicity 17603806 21800092 22678713 0 No evidence available 23794269 2016-10-12 MONDO:0012869 +ISCA-37488 22q11.2 recurrent region (distal type II, E-F) 22q11.22-q11.23 chr22:23119414-23649111 1 Little evidence for dosage pathogenicity 23765049 26278718 31837127 21278390 17351135 21948486 1 Little evidence for dosage pathogenicity 22140377 2023-01-19 +ISCA-37486 16p11.2 recurrent region (distal, BP2-BP3) (includes SH2B1) 16p11.2 chr16:28822635-29046499 3 Sufficient evidence for dosage pathogenicity 20808231 19966786 23258348 1 Little evidence for dosage pathogenicity 27240531 23258348 2017-03-09 MONDO:0013267 +ISCA-37483 19q13.3 region (PSG gene cluster) 19q13 chr19:43242796-43741310 40 Dosage sensitivity unlikely 40 Dosage sensitivity unlikely 2014-03-13 +ISCA-37481 3 copies: 16p centromere 16p11.1 chr16:34202088-35147508 40 Dosage sensitivity unlikely 40 Dosage sensitivity unlikely 2013-08-01 +ISCA-37480 3 copies: 15q telomere 15q26.3 chr15:102161480-102521392 0 No evidence available 40 Dosage sensitivity unlikely 2013-11-26 +ISCA-37478 15q11.2q13 recurrent (PWS/AS) region (Class 2,BP2-BP3) 15q11.2-q13.1 chr15:23747996-28379874 3 Sufficient evidence for dosage pathogenicity 7611294 22045295 3 Sufficient evidence for dosage pathogenicity 9106540 18374305 16840569 2013-11-26 MONDO:0008300 MONDO:0012081 +ISCA-37477 1 copy: 14q telomere; 3 copies: 14q telomere 14q32.3 chr14:106050000-107289540 40 Dosage sensitivity unlikely 40 Dosage sensitivity unlikely 2014-07-31 +ISCA-37476 14q11.2 region (TCRA region) 14q11.2 chr14:22111109-23021097 40 Dosage sensitivity unlikely 40 Dosage sensitivity unlikely 2015-04-09 +ISCA-37472 8p23.1 region (DEFB gene cluster) 8p23.1 chr8:7053186-8130689 40 Dosage sensitivity unlikely 40 Dosage sensitivity unlikely 2014-03-12 +ISCA-37471 1 copy: 6p telomere | 3 copies: 6p telomere 6p25 chr6:259528-339802 40 Dosage sensitivity unlikely 40 Dosage sensitivity unlikely 2014-06-20 +ISCA-37470 1 copy: 2q telomere|3 copies: 2q telomere 2q37.3 chr2:242930600-243102476 40 Dosage sensitivity unlikely 40 Dosage sensitivity unlikely 2014-04-24 +ISCA-37469 1q21.2 region (polymorphic region)(non-unique; also maps to chromosomes 16, 7, and others in GRCh38) 1q21.2 chr1:148867551-149768855 40 Dosage sensitivity unlikely 40 Dosage sensitivity unlikely 2020-10-22 +ISCA-37468 Xp11.23 region (includes MAOA and MAOB) Xp11.23 chrX:43514154-43741720 3 Sufficient evidence for dosage pathogenicity 22365943 20485326 23414621 0 No evidence available 2017-10-11 +ISCA-37467 7q36.3 ZRS (SHH cis-regulatory) duplication region (within LMBR1 intron 5) 7q36.3 chr7:156583796-156584568 0 No evidence available 3 Sufficient evidence for dosage pathogenicity 18178630 18417549 19291772 2018-02-14 MONDO:0008270 +ISCA-37449 14q32 region associated with UPD(14) phenotypes 14q32 chr14:100394594-101504529 2 Some evidence for dosage pathogenicity 20179077 18454453 0 No evidence available 2012-05-10 MONDO:0011975 +ISCA-37448 15q11.2 recurrent region (BP1-BP2) (includes NIPA1) 15q11.2 chr15:22832519-23090897 3 Sufficient evidence for dosage pathogenicity 31451536 24352232 30767844 31665216 40 Dosage sensitivity unlikely 2021-04-12 +ISCA-37446 22q11.2 recurrent (DGS/VCFS) region (proximal, A-D) (includes TBX1) 22q11.21 chr22:18912231-21465672 3 Sufficient evidence for dosage pathogenicity 20301696 27189754 3 Sufficient evidence for dosage pathogenicity 20301749 19254783 18414210 2018-08-31 MONDO:0008564 MONDO:0012020 +ISCA-37443 3q29 recurrent region (includes DLG1) 3q29 chr3:195756054-197344662 3 Sufficient evidence for dosage pathogenicity 2 Some evidence for dosage pathogenicity 18241066 18471269 24838842 2016-01-21 MONDO:0012269 MONDO:0012761 +ISCA-37442 6q24 region (includes PLAGL1) 6q24 chr6:144243292-144416561 1 Little evidence for dosage pathogenicity 16971482 3 Sufficient evidence for dosage pathogenicity 10615957 8842729 10923638 2016-05-24 MONDO:0011073 +ISCA-37441 11p11.2 (Potocki-Shaffer syndrome) region (includes ALX4, EXT2) 11p11.2 chr11:43894800-46152450 3 Sufficient evidence for dosage pathogenicity 15852040 16319823 20140962 0 No evidence available 2013-12-12 MONDO:0011022 +ISCA-37440 2p21 region (includes PREPL and SLC3A1) 2p21 chr2:44410272-44589641 30 Gene associated with autosomal recessive phenotype 11524703 16385448 18234729 0 No evidence available 2012-03-21 MONDO:0011669 +ISCA-37439 Xq28 recurrent region (includes GDI1) Xq28 chrX:153624564-153783898 0 No evidence available 3 Sufficient evidence for dosage pathogenicity 20004760 17546640 18047645 2016-05-26 MONDO:0010436 +ISCA-37438 14q11.2 region including CHD8 and SUPT16H 14q11.2 chr14:21826900-21861987 2 Some evidence for dosage pathogenicity 17545556 0 No evidence available 2012-05-09 +ISCA-37436 17p12 recurrent (HNPP/CMT1A) region (includes PMP22) 17p12 chr17:14097915-15422952 3 Sufficient evidence for dosage pathogenicity 20301566 3 Sufficient evidence for dosage pathogenicity 20301384 2016-10-13 MONDO:0008087 MONDO:0007309 +ISCA-37434 1p36 terminal region (includes GABRD) 1p36.33-p36.31 chr1:834083-6289973 3 Sufficient evidence for dosage pathogenicity 17918734 18245432 22766398 2 Some evidence for dosage pathogenicity 2016-05-31 MONDO:0011929 +ISCA-37433 22q11.2 recurrent (DGS/VCFS) region (proximal, A-B) (includes TBX1) 22q11.21 chr22:18912231-20287208 3 Sufficient evidence for dosage pathogenicity 20301696 27189754 26278718 3 Sufficient evidence for dosage pathogenicity 20301749 19254783 18414210 2018-08-31 MONDO:0008564 MONDO:0012020 +ISCA-37432 17q12 recurrent (RCAD syndrome) region (includes HNF1B) 17q12 chr17:34815072-36192489 3 Sufficient evidence for dosage pathogenicity 27929632 3 Sufficient evidence for dosage pathogenicity 26925472 30134084 27409573 26420380 2022-06-16 MONDO:0013797 MONDO:0013796 +ISCA-37431 17q11.2 recurrent region (includes NF1) 17q11.2 chr17:29097069-30264027 3 Sufficient evidence for dosage pathogenicity 20513137 20543202 22151963 2 Some evidence for dosage pathogenicity 22241097 18183042 25205021 2020-10-12 MONDO:0013357 MONDO:0030032 +ISCA-37430 17p13.3 (Miller-Dieker syndrome) region (includes YWHAE and PAFAH1B1) 17p13.3 chr17:1247833-2588909 3 Sufficient evidence for dosage pathogenicity 3391613, 1671808, 1879837, 7634541, 19584063, 12621583 3 Sufficient evidence for dosage pathogenicity 19136950 19520700 23813913 2016-11-09 MONDO:0009532 MONDO:0013182 +ISCA-37429 4p16.3 terminal (Wolf-Hirschhorn syndrome) region 4p16.3 chr4:331568-2010962 3 Sufficient evidence for dosage pathogenicity 2 Some evidence for dosage pathogenicity 2016-08-11 MONDO:0008684 +ISCA-37428 1q21.1 recurrent (TAR syndrome) region (proximal, BP2-BP3) (includes RBM8A) 1q21.1 chr1:145386507-145748064 1 Little evidence for dosage pathogenicity 22317977 25217958 1 Little evidence for dosage pathogenicity 22317977 25217958 2017-05-18 MONDO:0010121 +ISCA-37425 5q35 recurrent (Sotos syndrome) region (includes NSD1) 5q35.2-q35.3 chr5:175728979-177047793 3 Sufficient evidence for dosage pathogenicity 3 Sufficient evidence for dosage pathogenicity 23599694 23913520 24819041 2014-04-10 MONDO:0019349 +ISCA-37424 10q22.3q23.2 recurrent region (includes BMPR1A) 10q22.3-q23.2 chr10:81682843-88739388 3 Sufficient evidence for dosage pathogenicity 31561016 24550761 28588438 21248748 23057600 1 Little evidence for dosage pathogenicity 21248748 26383923 22043167 2023-05-15 +ISCA-37423 8p23.1 recurrent region (includes GATA4) 8p23.1 chr8:8100064-11766329 3 Sufficient evidence for dosage pathogenicity 20969981 23239632 19606479 2 Some evidence for dosage pathogenicity 26097203 21933911 23165946 2022-06-10 +ISCA-37421 1q21.1 recurrent region (BP3-BP4, distal) (includes GJA5) 1q21.1-q21.2 chr1:146577486-147394506 3 Sufficient evidence for dosage pathogenicity 3 Sufficient evidence for dosage pathogenicity 22199024 23018752 2016-04-14 MONDO:0012914 MONDO:0012915 +ISCA-37420 17q21.3 recurrent region (includes KANSL1) 17q21.3 chr17:43705166-44164880 3 Sufficient evidence for dosage pathogenicity 20301783 18628315 1 Little evidence for dosage pathogenicity 19502243 24649381 26565673 2020-08-10 MONDO:0012496 +ISCA-37418 17p11.2 recurrent (SMS/PLS) region (includes RAI1) 17p11.2 chr17:16810028-20213202 3 Sufficient evidence for dosage pathogenicity 3 Sufficient evidence for dosage pathogenicity 17357070 20188345 2013-11-21 MONDO:0008434 MONDO:0012574 +ISCA-37417 Xp22.31 recurrent region (includes STS) Xp22.31 chrX:6455812-8124954 3 Sufficient evidence for dosage pathogenicity 40 Dosage sensitivity unlikely 2021-07-01 MONDO:0010622 +ISCA-37415 16p13.11 recurrent region (BP2-BP3) (includes MYH11) 16p13.11 chr16:15511711-16292265 3 Sufficient evidence for dosage pathogenicity 18550696 19843651 24246141 2 Some evidence for dosage pathogenicity 30767844 24352232 30287593 2021-04-12 +ISCA-37411 15q13.3 recurrent region (BP4-BP5) (includes CHRNA7) 15q13 chr15:31192889-32445405 3 Sufficient evidence for dosage pathogenicity 18278044 19289393 19136953 1 Little evidence for dosage pathogenicity 19372089 18805830 26997942 2018-04-27 MONDO:0012774 +ISCA-37409 16p12.2 recurrent region (proximal) (includes EEF2K, CDR2) 16p12.2 chr16:21948445-22430804 2 Some evidence for dosage pathogenicity 20154674 24163246 23682798 0 No evidence available 2018-03-23 +ISCA-37408 2p15p16.1 region (includes BCL11A) 2p15-p16.1 chr2:59139200-62488871 3 Sufficient evidence for dosage pathogenicity 16963482 18245392 22579565 1 Little evidence for dosage pathogenicity 22726847 26278498 2016-06-08 MONDO:0012916 +ISCA-37406 16p13.3 region (includes CREBBP) 16p13.3 chr16:3775056-3930121 3 Sufficient evidence for dosage pathogenicity 1 Little evidence for dosage pathogenicity 2016-06-09 MONDO:0012519 +ISCA-37405 2q13 recurrent region (includes NPHP1) 2q13 chr2:110862108-110983703 30 Gene associated with autosomal recessive phenotype 40 Dosage sensitivity unlikely 2016-02-25 +ISCA-37404 15q11.2q13 recurrent (PWS/AS) region (Class 1, BP1-BP3) 15q11.2-q13.1 chr15:22832519-28379874 3 Sufficient evidence for dosage pathogenicity 7611294 22045295 3 Sufficient evidence for dosage pathogenicity 9106540 18374305 16840569 2013-11-26 MONDO:0008300 MONDO:0012081 +ISCA-37401 11p13 (WAGR syndrome) region 11p13 chr11:31803509-32510988 3 Sufficient evidence for dosage pathogenicity 1 Little evidence for dosage pathogenicity 23701296 2016-05-24 MONDO:0008681 +ISCA-37400 16p11.2 recurrent region (proximal, BP4-BP5) (includes TBX6) 16p11.2 chr16:29649997-30199852 3 Sufficient evidence for dosage pathogenicity 20301775 18184952 21841781 3 Sufficient evidence for dosage pathogenicity 18184952 21731881 21841781 2017-02-09 MONDO:0012756 MONDO:0013847 +ISCA-37397 22q11.2 recurrent region (distal type I, D-E/F) 22q11.21-q11.22 chr22:21917117-23649111 3 Sufficient evidence for dosage pathogenicity 23765049 30524331 26141236 18179902 1 Little evidence for dosage pathogenicity 22140377 19193630 18414210 2022-12-08 MONDO:0012740 +ISCA-37396 15q24 recurrent region (LCR A-LCR D) (includes SIN3A) 15q24.1-q24.2 chr15:72963715-75972909 3 Sufficient evidence for dosage pathogenicity 22180641 19557438 19233321 1 Little evidence for dosage pathogenicity 2018-08-31 MONDO:0013672 +ISCA-37394 2q37.3 terminal region (includes HDAC4) 2q37.3 chr2:239954693-242930600 3 Sufficient evidence for dosage pathogenicity 19752160 23188045 25402011 0 No evidence available 2016-06-13 MONDO:0010886 +ISCA-37393 22q11.21 recurrent (Cat eye syndrome) region (includes CECR2) 22q11.1-q11.21 chr22:17392953-18591860 0 No evidence available 16708226 3 Sufficient evidence for dosage pathogenicity 22890013 22495764 11693792 2014-02-27 MONDO:0007276 +ISCA-37392 7q11.23 recurrent (Williams-Beuren syndrome) region (includes ELN) 7q11.23 chr7:72744455-74142510 3 Sufficient evidence for dosage pathogenicity 20301427 3 Sufficient evidence for dosage pathogenicity 26610320 2015-08-06 MONDO:0008678 MONDO:0012342 +ISCA-37390 5p15 terminal (Cri du chat syndrome) region 5p15.33-p15.2 chr5:37693-11347262 3 Sufficient evidence for dosage pathogenicity 15635506 11238681 2 Some evidence for dosage pathogenicity 2016-06-21 MONDO:0007404 diff --git a/tests/regions/clingen/rocksdb/000014.sst b/tests/regions/clingen/rocksdb/000014.sst new file mode 100644 index 00000000..e29027a5 --- /dev/null +++ b/tests/regions/clingen/rocksdb/000014.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:23d2221708f96b293b70b914760af4f46ea3909755413c4761132adc94cef5cc +size 1335 diff --git a/tests/regions/clingen/rocksdb/000016.sst b/tests/regions/clingen/rocksdb/000016.sst new 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