Number of variants imported from various external resources. The first block refers to sequencing/genotyping studies, the second to sample-independent annotation databases. "Unique to study" counts variants that were observed only in that particular study. "Variants passed" refers to variants that passed quality metrics as defined by the particular study, at least one sample has to pass; n/a: individual sample quality metrics not available. Totals exclude duplicates seen in different studies. Variants in annotation databases are included only if they can be mapped to precise coordinates and allele. Since a large proportion of the variants discovered by literature mining are given at the protein level only, they were not compared to other studies. *dbNSFP contains hypothetical variants, see text. †ExAC includes samples from 1000 Genomes, ESP6500, and TCGA. ‡Note that data from HGMD, PharmGKB, UK10K diseases and TCGA germline are not visible to external users on the RVS website. #Counts for SwissVar refer to distinct amino acid changes.
Last update: September 21 2015, 15:01.
Variant types and effects
Effects of observed variants. Shown are the numbers of variants that fall into a specific category of the SequenceOntology, as determined by snpEff. Counts are based on observations in studies with ≤500 samples, unfiltered, and take into account one canonical transcript per variant. Regions up/downstream of a gene are limited to 5000bp. '+' indicates that a variant falls into multiple categories, such as an inframe insertion that leads to the gain of a stop codon.