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Data provided by the variant annotator is the result of integrating most of the annotations available at the CellBase knowledge base: ENSEMBL's core transcript annotation such as location, id, strand, biotype,etc.; protein annotation provided by UniProt, InterPro, SIFT and PolyPhen; population frequencies provided by the European Variation Archive for The 1000 Genomes Project Phase 3, The Exome Server Project (EVS), The Exome Aggregation Consortium v3 (ExaC) and The Genomes of the Netherlands (GoNL); sequence conservation from PhastCons and PhyloP; gene expression values from The Genome Expression Atlas and The Genotype-Tissue Expression project (GTEx); gene drug interaction data from The Drug Gene Interaction Database (DGIdb) and the Human Phenotype Ontology database (HPO); clinical variants annotation from ClinVar and The Catalogue of Somatic Mutations in Cancer (COSMIC). Sequence effect prediction is also calculated on the fly and described by Sequence Ontology (SO) terms. We are constantly working to integrate new data sources in the knowledgebase.
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