Resource

Id:hg38/scores/clinvar_20221105
Type:allele_score
Summary: ClinVar resource downloaded on 2022-11-05. Chromosome names are remapped to have `chr` prefix. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible
Description:

ClinVar resource downloaded on 2022-11-05. Chromosome names are remapped to have chr prefix.

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible
Labels:
  • reference_genome: hg38/genomes/GRCh38-hg38

Scores

id type default annotation description histogram range
AF_ESP float

AF_ESP

 allele frequencies from GO-ESP HISTOGRAM FOR AF_ESP [0.000, 1.000]
AF_EXAC float

AF_EXAC

 allele frequencies from ExAC HISTOGRAM FOR AF_EXAC [0.000, 1.000]
AF_TGP float

AF_TGP

 allele frequencies from TGP HISTOGRAM FOR AF_TGP [0.000, 1.000]
ALLELEID int

ALLELEID

 the ClinVar Allele ID HISTOGRAM FOR ALLELEID [15041.000, 1780011.000]
CLNDN str

CLNDN

 ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB NO HISTOGRAM NO DOMAIN
CLNDNINCL str

CLNDNINCL

 For included Variant : ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB NO HISTOGRAM NO DOMAIN
CLNDISDB str

CLNDISDB

 Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN NO HISTOGRAM NO DOMAIN
CLNDISDBINCL str

CLNDISDBINCL

 For included Variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN NO HISTOGRAM NO DOMAIN
CLNHGVS str

CLNHGVS

 Top-level (primary assembly, alt, or patch) HGVS expression. NO HISTOGRAM NO DOMAIN
CLNREVSTAT str

CLNREVSTAT

 ClinVar review status for the Variation ID HISTOGRAM FOR CLNREVSTAT criteria_provided,_single_submitter, criteria_provided,_multiple_submitters,_no_conflicts, criteria_provided,_conflicting_interpretations, no_assertion_criteria_provided, reviewed_by_expert_panel, no_assertion_provided, no_interpretation_for_the_single_variant, practice_guideline
CLNSIG str

CLNSIG

 Clinical significance for this single variant; multiple values are separated by a vertical bar HISTOGRAM FOR CLNSIG Uncertain_significance, Likely_benign, Benign, Pathogenic, Conflicting_interpretations_of_pathogenicity, Likely_pathogenic, Benign/Likely_benign, Pathogenic/Likely_pathogenic, not_provided, drug_response, other, risk_factor, association, Affects, Pathogenic|_other, Pathogenic|_drug_response, protective, Pathogenic|_risk_factor, Conflicting_interpretations_of_pathogenicity|_other, Likely_pathogenic|_drug_response, Conflicting_interpretations_of_pathogenicity|_risk_factor, Benign|_other, Likely_benign|_other, confers_sensitivity, Likely_pathogenic|_risk_factor, Uncertain_risk_allele, Pathogenic/Likely_pathogenic|_other, Pathogenic|_Affects, Uncertain_significance|_drug_response, Benign/Likely_benign|_other, Pathogenic|_association, Uncertain_significance|_risk_factor, Benign|_risk_factor, Conflicting_interpretations_of_pathogenicity|_association, Likely_benign|_drug_response|_other, Likely_risk_allele, Pathogenic/Likely_pathogenic|_risk_factor, Uncertain_significance|_association, Likely_pathogenic|_Affects, Likely_pathogenic|_association, Uncertain_significance|_other, protective|_risk_factor, Benign/Likely_benign|_risk_factor, Conflicting_interpretations_of_pathogenicity|_other|_risk_factor, Likely_pathogenic|_other, Pathogenic/Likely_pathogenic|_drug_response, Pathogenic|_protective, drug_response|_risk_factor, Affects|_association, Benign/Likely_benign|_drug_response, Benign|_association, Benign|_confers_sensitivity, Benign|_drug_response, Conflicting_interpretations_of_pathogenicity|_association|_risk_factor, Conflicting_interpretations_of_pathogenicity|_drug_response, Likely_pathogenic,_low_penetrance, association_not_found, Affects|_risk_factor, Benign/Likely_benign|_association, Benign/Likely_benign|_drug_response|_other, Benign/Likely_benign|_other|_risk_factor, Benign|_association|_confers_sensitivity, Benign|_protective, Conflicting_interpretations_of_pathogenicity|_Affects, Conflicting_interpretations_of_pathogenicity|_drug_response|_other, Conflicting_interpretations_of_pathogenicity|_protective, Likely_benign|_risk_factor, Pathogenic/Likely_risk_allele, Pathogenic|_association|_protective, Pathogenic|_confers_sensitivity, Pathogenic|_drug_response|_other, Uncertain_risk_allele|_protective, Uncertain_risk_allele|_risk_factor, Uncertain_significance|_Affects, association|_drug_response|_risk_factor, association|_risk_factor, drug_response|_other
CLNSIGCONF str

CLNSIGCONF

 Conflicting clinical significance for this single variant; multiple values are separated by a vertical bar NO HISTOGRAM NO DOMAIN
CLNSIGINCL str

CLNSIGINCL

 Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance; multiple values are separated by a vertical bar NO HISTOGRAM NO DOMAIN
CLNVC str

CLNVC

 Variant type HISTOGRAM FOR CLNVC single_nucleotide_variant, Deletion, Duplication, Microsatellite, Indel, Insertion, Inversion, Variation, copy_number_loss, copy_number_gain
CLNVCSO str

CLNVCSO

 Sequence Ontology id for variant type HISTOGRAM FOR CLNVCSO SO:0001483, SO:0000159, SO:1000035, SO:0000289, SO:1000032, SO:0000667, SO:1000036, SO:0001059, SO:0001743, SO:0001742
CLNVI str

CLNVI

 the variant's clinical sources reported as tag-value pairs of database and variant identifier NO HISTOGRAM NO DOMAIN
DBVARID str

DBVARID

 nsv accessions from dbVar for the variant NO HISTOGRAM NO DOMAIN
GENEINFO str

GENEINFO

 Gene(s) for the variant reported as gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|) NO HISTOGRAM NO DOMAIN
MC str

MC

 comma separated list of molecular consequence in the form of Sequence Ontology ID|molecular_consequence NO HISTOGRAM NO DOMAIN
ORIGIN str

ORIGIN

 Allele origin. One or more of the following values may be added: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other HISTOGRAM FOR ORIGIN 1, 0, 32, 2, 4, 5, 33, 16, 17, 8, 9, 3, 128, 129, 64, 65, 25, 21, 13, 35, 49, 20, 24, 12, 37, 41, 29, 69, 34, 513, 28, 48, 512, 7, 11, 36, 53, 133, 19, 73, 145, 1024, 93, 18, 40, 81, 1025, 137, 161, 45, 51, 6, 61, 68, 89, 132, 144, 43, 57, 85, 10, 131, 136, 153, 27, 39, 515, 517, 544, 545, 72, 77, 80
RS str

RS

 dbSNP ID (i.e. rs number) NO HISTOGRAM NO DOMAIN
SSR int

SSR

 Variant Suspect Reason Codes. One or more of the following values may be added: 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other NO HISTOGRAM NO DOMAIN

Files

Filename Size md5
chr_rename.txt 203.0 B 6b381222aba146516fd282587ed8598d
clinvar_20221105.vcf.gz 56.57 MB 48ef344c7120566088450abbd9b03b3a
clinvar_20221105.vcf.gz.dvc 95.0 B d08b2c9d458728873976154de56e977e
clinvar_20221105.vcf.gz.tbi 323.08 KB 1a0236efda3814b788a72d8a519bcce7
clinvar_20221105.vcf.gz.tbi.dvc 97.0 B b13efe1916ba28c569680903ef7374b9
clinvar_20221105_chr.header.vcf.gz 1.33 KB 0004a6cee60b4e8d76185a9f8b9a550a
clinvar_20221105_chr.header.vcf.gz.tbi 80.0 B e7180bb953d2bd657c420a5f76a7164d
clinvar_20221105_chr.vcf.gz 57.9 MB d2f167e0c1155e416baf545205ed17b1
clinvar_20221105_chr.vcf.gz.dvc 99.0 B 4bf30688e4fb884644fb5806d2679268
clinvar_20221105_chr.vcf.gz.tbi 320.76 KB d1e6cc2b74018dfc994d3da648b591f6
clinvar_20221105_chr.vcf.gz.tbi.dvc 101.0 B e067c10134471aa904d5aa815311b27a
genomic_resource.yaml 1.3 KB 3816a882b8d382135a0c225e868aa772
statistics/