The Global Human Genomics Community

70+ Genomic Databases

VarSome offers a massive cross-referenced knowledge base consisting of 70+ genomic databases, representing over 33 billion data points. But there is more to it: whenever a public database is updated, VarSome processes it and makes it available to the whole genomics community for annotation and classification!

VarSome.com Resources: CGD, HGNC, Ensembl, RefSeq, UniGene, CIViC genes, dbSNP, GERP, ClinVar, IARC TP53 germline, IARC TP53 somatic, ICGC germline, ICGC somatic, Kaviar, gnomAD Exomes, gnomAD Genomes, DANN scores, CIViC mutations, HPO, UniProt variants, UniProt domains, GWAS Catalog, GHR, DGV, DECIPHER, ClinVar, ExAC CNVs, PanelApp, MONDO, PMKB, DOMINO, GDC, Bravo, MitoMap, SIFT, SIFT4G, PROVEAN, LRT, MutationTaster, MutationAssessor, FATHMM, fitCons, MetaSVM and MetaLR, Eigen & Eigen PC, M-CAP, REVEL, MutPred, MVP, MPC, PrimateAI, deogen2, ALoFT, phyloP, phastCons, bStatistic, GTEx, UniProt Genes, BioCarta Pathway, ConsensusPathDB, KEGG pathway, GDI, LoFTool, Essential genes, GHIS, RVIS, HIPred, P(HI) Score, P(rec) Score, GNF/Atlas Expressions, Gene Ontology.

Please note that with VarSome Clinical you can access proprietary and licensed datasets of some 3rd party data providers, although you still need to obtain a corresponding license. You can also import your own local database with allele frequencies and integrate it privately in your VarSome Clinical account for annotation and ACMG classification of your variants.

AACT, DGIdb, COSMIC, Polyphen-2, PharmGKB, CGD, HGNC, Ensembl, RefSeq, UniGene, CIViC genes, dbSNP, GERP, ClinVar, IARC TP53 germline, IARC TP53 somatic, ICGC germline, ICGC somatic, Kaviar, gnomAD Exomes, gnomAD Genomes, DANN scores, CIViC mutations, HPO, UniProt variants, UniProt domains, GWAS Catalog, GHR, DGV, DECIPHER, ClinVar, ExAC CNVs, PanelApp, MONDO, PMKB, DOMINO, GDC, Bravo, MitoMap, SIFT, SIFT4G, PROVEAN, LRT, MutationTaster, MutationAssessor, FATHMM, fitCons, MetaSVM and MetaLR, Eigen & Eigen PC, M-CAP, REVEL, MutPred, MVP, MPC, PrimateAI, deogen2, ALoFT, phyloP, phastCons, bStatistic, GTEx, UniProt Genes, BioCarta Pathway, ConsensusPathDB, KEGG pathway, GDI, LoFTool, Essential genes, GHIS, RVIS, HIPred, P(HI) Score, P(rec) Score, GNF/Atlas Expressions, Gene Ontology

Community

VarSome.com is a community-driven project aimed at sharing global expertise on human genomic variants. It's features a variant search engine and aggregated knowledge base consisting of more than 70 cross-referenced data resources, as well as real-time functional annotation of any variant.

Its world-wide community of more than 300,000 healthcare and life sciences professionals, who classify, link research findings and publications, and share evidence on variants, creating a unique resource in the genomics landscape. VarSome.com also facilitates introductions between users who wish to exchange notes on search results, without compromising strict privacy policies of both parties.

Versatile Variant Search

You can search VarSome.com by HGVS nomenclature, rsID, gene name, transcript symbol or genomic location. VarSome.com can also parse single lines from VCF files to look up the variant they describe. The results are not limited to known variants, you can query any possible variant.

Please note that with VarSome Clinical you can annotate an entire VCF and FASTQ files, and generate a clinical report for your NGS data.

Full-text Search

VarSome.com's full-text search functions like other search engines with one important difference: the search query returns only entries from the VarSome.com aggregated knowledge base, thus showing you only the results you are looking for. It enables you to perform targeted searches not just for variants, but over the entire contents of VarSome.com, such as articles, diseases, phenotypes, genes, etc. Importantly, this includes content provided by the entire VarSome.com user global community.

ACMG Classification

VarSome.com displays automated variant classification according to the guidelines of the American College of Medical Genetics and Genomics (Richards et al. 2015). Each ACMG rule is explained, along with why it has been triggered, or why not. If you have additional evidence, you can manually turn on other ACMG rules and easily reach the final verdict for your variant.

Please note that with VarSome Clinical, the clinically-certified edition of VarSome.com for clinicians and molecular geneticists, you can also import your own list of preferred transcripts and local database with allele frequencies and use it for variant annotation and ACMG classification.

Application Programming Interface (API)

VarSome.com provides a powerful API which allows you to integrate its knowledge base into your own software at a fraction of the cost it would take to integrate data from such a multitude of sources and perform real-time functional annotation.

Cite VarSome!

If you use VarSome.com for your work please cite it in your articles and all other communications.

VarSome: The Human Genomic Variant Search Engine. Christos Kopanos, Vasilis Tsiolkas, Alexandros Kouris, Charles E Chapple, Monica Albarca Aguilera, Richard Meyer, and Andreas Massouras. Oxford Bioinformatics, bty897, 30 October 2018. doi: https://doi.org/10.1093/bioinformatics/bty897