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. 2016 Jan 4;44(D1):D862-8.
doi: 10.1093/nar/gkv1222. Epub 2015 Nov 17.

ClinVar: public archive of interpretations of clinically relevant variants

Melissa J Landrum  1 , Jennifer M Lee  2 , Mark Benson  2 , Garth Brown  2 , Chen Chao  2 , Shanmuga Chitipiralla  2 , Baoshan Gu  2 , Jennifer Hart  2 , Douglas Hoffman  2 , Jeffrey Hoover  2 , Wonhee Jang  2 , Kenneth Katz  2 , Michael Ovetsky  2 , George Riley  2 , Amanjeev Sethi  2 , Ray Tully  2 , Ricardo Villamarin-Salomon  2 , Wendy Rubinstein  2 , Donna R Maglott  2
Affiliations

ClinVar: public archive of interpretations of clinically relevant variants

Melissa J Landrum et al. Nucleic Acids Res. .

Abstract

ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) at the National Center for Biotechnology Information (NCBI) is a freely available archive for interpretations of clinical significance of variants for reported conditions. The database includes germline and somatic variants of any size, type or genomic location. Interpretations are submitted by clinical testing laboratories, research laboratories, locus-specific databases, OMIM®, GeneReviews™, UniProt, expert panels and practice guidelines. In NCBI's Variation submission portal, submitters upload batch submissions or use the Submission Wizard for single submissions. Each submitted interpretation is assigned an accession number prefixed with SCV. ClinVar staff review validation reports with data types such as HGVS (Human Genome Variation Society) expressions; however, clinical significance is reported directly from submitters. Interpretations are aggregated by variant-condition combination and assigned an accession number prefixed with RCV. Clinical significance is calculated for the aggregate record, indicating consensus or conflict in the submitted interpretations. ClinVar uses data standards, such as HGVS nomenclature for variants and MedGen identifiers for conditions. The data are available on the web as variant-specific views; the entire data set can be downloaded via ftp. Programmatic access for ClinVar records is available through NCBI's E-utilities. Future development includes providing a variant-centric XML archive and a web page for details of SCV submissions.

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Figures

Figure 1.
Figure 1.
The default web display in ClinVar is the variation-specific page. The top section of the page describes the variant or set of variants being interpreted and highlights the aggregate clinical significance that was calculated. It also includes summary information about conditions reported for the variant and genes that are affected by the variant.
Figure 2.
Figure 2.
The lower portion of the ClinVar variation page presents the details of submitted interpretations in three tabs. The first tab displays a summary of the interpretations asserted by each submitter, including the submitted clinical significance, the date the significance was last evaluated, the reported condition, and the submitting organization.
Figure 3.
Figure 3.
(A) The evidence submitted to ClinVar is presented on two tabs. The Summary Evidence tab provides a summary of the evidence provided by each submitting organization, including the number of families and individuals observed with the variant, and summary values for allele origin, ethnicity and geographic origin. (B) The Supporting Observations tab provides the details of each observation submitted by each organization. The observation may be specific to an individual or to an aggregate group of individuals, and includes specific values for allele origin, ethnicity and geographic origin, as well as observed phenotypes.
See this image and copyright information in PMC

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