Sources of data in ClinVar
ClinVar is built from data provided by submitters. ClinVar is not staffed to review the literature to build content via curation. We gratefully acknowledge all those who contribute their data. This document cannot acknowledge all our contributors explicitly; our submitters page provides more explicit attribution. This document summarizes some of the major categories of submitters, and how submissions in those categories are processed.
Practice guidelines/Professional societies
Groups that provide practice guidelines for specific variants may apply for recognition as such by ClinGen. If the application is approved, classifications provided by that submitter will have precedence over all others, and will be represented with a review status of 4 stars . All submissions with that status can be retrieved by applying the filter Practice guideline .
Expert panels
Groups that review evidence about the classifications of variants may apply for recognition from ClinGen as an expert panel. If the application is approved, classifications provided by that submitter will have precedence over those not from an expert panel or professional guideline, and will be represented with a review status of 3 stars . All submissions with that status can be retrieved by applying the filter Expert panel .
Documentation supporting each expert panel is provided on our FTP site .
Genetic testing laboratories
Clinical genetic testing laboratories submit data about variants identified during their testing, with related literature and other evidence that contributed to the classification.
Locus-specific databases
Locus-specific databases have submitted information about the variants they have processed, often with links to the literature and summary data. ClinVar provides links back to those databases by allele. We look forward to expanding this data set.
Research studies
ClinSeq ® , PubMed 22703879 was the first group to request ClinVar accessions pre-publication.
Semi-automatic data flows
OMIM®
NCBI updates data from OMIM® daily. This includes information about diseases, genes, and allelic variants. The content is used to maintain the query interface which directs results to omim.org, to integrate information about diseases and their related genes for Gene, GTR, and MedGen, and to identify allelic variant data for ClinVar. The description of the allelic variant is mined to extract complete HGVS expressions when text includes one nucleotide accession with version and a representation of the sequence change, within parentheses. As resources allow, the remainder of allelic variants are evaluated by curators to establish a molecular description.
GeneReviews®
The molecular genetics section of novel and updated GeneReviews® are evaluated for submission to ClinVar as part of GeneReviews' editorial processing. This includes any documents submitted as part of a GeneReview® but not incorporated into the article explicitly. ClinVar encourages authors of GeneReviews® to submit information about variants to ClinVar directly. See how to submit.
Other public databases
UniProtKB
UniProt has submitted information about variants to NCBI databases, partially in conjunction with the RefSeqGene/LRG collaboration. The submissions are not comprehensive, but the links to the variant pages, e.g. http://web.expasy.org/variant_pages/VAR_069097.html, can be useful in bridging between nucleotide-specific and protein-specific information.
UniProt has also begun to connect AlleleIDs in ClinVar to their VAR identifiers. By so doing, ClinVar is now reporting the HGVS expressions anchored on UniProt sequences that UniProt provided. Links are also provided to the variant section of a UniProt record, e.g. P78363#VAR_008401.