dbVar — Database of Genomic Structural Variation

Overview

dbVar is the NCBI open-access archive for human genomic structural variation, the large-scale variants over 50 base pairs that include copy number variants, insertions, deletions, inversions, mobile elements, translocations, and complex rearrangements. It is the structural-variant complement to dbSNP, which holds small-scale variants, and together with the controlled-access dbGaP and the clinical archive ClinVar it forms NCBI’s division of variant data by scale and sensitivity. Maintained by NCBI at the NIH, dbVar holds over 5 million submitted structural variants from more than 150 human studies, assigns accession numbers at the study, variant-region, and supporting-call levels, and provides curated reference sets such as the Genome in a Bottle benchmark callset and tracks of clinical and common structural variants. Since November 2017 it has accepted human data only, with existing non-human records retained on FTP. Its data is openly browsable, downloadable, and viewable as track hubs in genome browsers.

Accessioning collaboration

dbVar accessions structural variants jointly with two international partners under a shared data model: the DGVa (Database of Genomic Variants archive) at EMBL-EBI and the TogoVar-repository at DDBJ in Japan. Accessions are prefixed by the processing centre, with nsv and nstd assigned by NCBI (dbVar), esv and estd by EMBL-EBI (DGVa), and dsv and dstd by DDBJ. This tripartite arrangement mirrors the INSDC division of sequence-read archiving across NCBI, EMBL-EBI, and DDBJ.

Connections

• relatedTo: dbSNP (NCBI sibling archive; dbVar holds structural variants over 50 bp while dbSNP holds small variants)
• relatedTo: EVA (EMBL-EBI variant archive; the DGVa structural-variation archive at EMBL-EBI co-accessions structural variants with dbVar under a shared data model)
• relatedTo: ClinVar (clinically relevant structural variants are directed to ClinVar for interpretation)
• relatedTo: DDBJ (the TogoVar-repository at DDBJ is the third structural-variant accessioning partner)

Resources

• https://www.ncbi.nlm.nih.gov/dbvar/
• https://www.ncbi.nlm.nih.gov/dbvar/content/help/ (Help and FAQ)
• https://github.com/ncbi/dbvar (curated structural-variant reference sets)
• https://www.re3data.org/repository/r3d100010786 (re3data registry entry)