30+ Genomic Databases
VarSome offers a massive cross-referenced knowledge base consisting of 30+ public 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!
Integrated resources: ClinVar, dbSNP, gnomAD, HPO, MONDO, Ensembl, RefSeq, GWAS, CGD, HGNC, UniGene, Orphanet, CIViC genes, GERP, dbNSFP, COSMIC, IARC TP53, ICGC, Kaviar, DANN scores, CIViC mutations, UniProt variants, UniProt domains, GHR, CPIC, DGV, DECIPHER, ExAC CNVs, ExAC genes, PanelApp, Mondo, PMKB.
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 VarSome for annotation and ACMG classification of your variants.
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Versatile Variant Search
You can search VarSome by HGVS nomenclature, rsID, gene name, transcript symbol or genomic location. VarSome 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 Pro and VarSome Clinical you can annotate an entire VCF and FASTQ files, correspondingly. While VarSome Pro is a variant interpretation tool for researchers, VarSome Clinical is a fully-fledged clinically-certified platform for analysis of NGS data.
See query examples
VarSome full-text search functions like other search engines with one important difference: the search query returns only entries from the VarSome aggregated knowledge base, thus showing you only the results your are looking for. It enables you to perform targeted searches not just for variants, but over the entire contents of VarSome, such as articles, diseases, phenotypes, genes, etc. Importantly, this includes content provided by the entire VarSome user global community.
More about Full Text Search
VarSome 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 for clinicians and molecular geneticists, you can also import your own local database with allele frequencies and use it for variant annotation and ACMG classification.
More about ACMG Classification
Application Programming Interface (API)
VarSome provides a powerful API which allows you to integrate its knowledge base in your own software at a fraction of the cost that would take to integrate data from such a multitude of sources and perform real-time functional annotation.
Learn more about VarSome API
If you use VarSome 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
Read the VarSome paper