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Table 3 Examples of disease and population databases

From: Variants of uncertain significance in the era of high-throughput genome sequencing: a lesson from breast and ovary cancers

ToolsWebsiteDescription
ClinVarhttps://www.ncbi.nlm.nih.gov/clinvar/Freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence.
ClinVar Minerhttps://clinvarminer.genetics.utah.edu/Interface for viewing ClinVar data. Complements the existing ClinVar database by enabling exploration of the data at different levels of granularity and from different perspectives. Statistics for current data and for historical data can be viewed relative to all submissions, submitters, conflicting submissions and genes.
dbSNPhttps://www.ncbi.nlm.nih.gov/snp/Public-domain archive for a broad collection of simple genetic polymorphisms. This collection includes single-base substitutions, small-scale multi-base “indels”, and retroposable element insertion and microsatellite repeat variations.
Leiden Open Variation Database (LOVD)http://www.lovd.nl/3.0/homeFlexible, freely available tool for gene-centered collection and display of DNA variants.
Cosmichttps://cancer.sanger.ac.uk/cosmicSource of expert manually curated somatic mutation information relating to human cancers.
cBioPortalhttps://www.cbioportal.org/Open-access, open-source resource for interactive exploration of multidimensional cancer genomics datasets. Stores non-synonymous mutations, DNA copy-number data, mRNA and microRNA expression data, protein-level and phosphoprotein level data, DNA methylation data, and de-identified clinical data.
BRCA Exchangehttps://brcaexchange.org/Open-access web portal resource to display BRCA1/2 variants drawn from global sources and to enable BRCA1/2 variants to be expert reviewed, interpreted, classified, and aggregated in an integrated data system. The publicly accessible display of these classifications, with supporting evidence, facilitates accurate understanding of the clinical relevance of any individual BRCA1/2 variant.
GnomADhttps://gnomad.broadinstitute.org/Resource with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available.
Exome sequencing projecthttps://evs.gs.washington.edu/EVS/Database for discovering novel genes and disease mechanisms by pioneering the application of NGS of the protein coding regions of the human genome across diverse, richly-phenotyped populations.
1000Genomeshttps://www.internationalgenome.org/Public catalogue of human variation and genotype data for inferring a large complement of variants, including “indels” and structural variants, in panels of people worldwide for whom only a small subset of SNPs have been analyzed, using partial sequencing techniques such as genotyping arrays.
Human Gene Mutation Databasehttp://www.hgmd.cf.ac.uk/ac/index.phpUp-to-date and comprehensive reference source to the spectrum of inherited human gene lesions. It includes the first example of all mutations causing or associated with human inherited disease, plus disease-associated/functional polymorphisms reported in the literature.
Human Genome Variation Societyhttps://www.hgvs.org/Source for the discovery and characterization of genomic variations including population distribution and phenotypic associations, by promoting collection, documentation and free distribution of genomic variation information and associated clinical variations.
  1. “indel” = insertion and/or deletion. Database and algorithm descriptions were taken from respective websites.