Abstract
Clinical genetic testing has exponentially expanded in recent years, leading to an overwhelming amount of patient variants with high variability in pathogenicity and heterogeneous phenotypes. A large part of the variant level data is aggregated in public databases such as ClinVar. However, the ability to explore this rich resource and answer general questions such as ‘How many genes inside ClinVar are associated with a specific disease? or ‘In which part of the protein are patient variants located?’ is limited and requires advanced bioinformatics processing. Here, we present Simple ClinVar (http://simple-clinvar.broadinstitute.org/) a web server application that is able to provide variant, gene and disease level summary statistics based on the entire ClinVar database in a dynamic and user-friendly web-interface. Overall, our web application is able to interactively answer basic questions regarding genetic variation and its known relationships to disease. By typing a disease term of interest, the user can identify in seconds the genes and phenotypes most frequently reported to ClinVar. Subsets of variants can then be further explored, filtered or mapped and visualized in the corresponding protein sequences. Our website will follow ClinVar monthly releases and provide easy access to ClinVar resources to a broader audience including basic and clinical scientists.
Highlights
In recent years, clinical genetic testing has expanded exponentially alongside transparent and persistent data sharing.ClinVar is a public database of variant interpretations (1) that has steadily grown to become the largest publicly available genetic variant database and provides an ever-growing resource to study genotype–phenotype correlations
Simple ClinVar works over the pre-filtered version of the ClinVar database
DIRECTIONS ClinVar stands out today as one of the largest catalogs of genetic variants clinically associated with disease
Summary
Clinical genetic testing has expanded exponentially alongside transparent and persistent data sharing. ClinVar is a public database of variant interpretations (1) that has steadily grown to become the largest publicly available genetic variant database and provides an ever-growing resource to study genotype–phenotype correlations. The database is populated by a broad range of submitters including but not limited to researchers, clinicians, laboratories and genetic counselors (1). Most data are derived from clinical genetic testing laboratories. Since its inception in 2013, ClinVar has grown rapidly As of 22 April 2019, ClinVar contains 503 065 unique genetic variants from 1229 submitters from all around the world. ClinVar has become a valuable resource to support clinical variant interpretation (2)
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