Variant Effect Predictor

This component determines the effect of genetic variants using Ensembl's Variant Effect Predictor (VEP) via their REST API (https://rest.ensembl.org/#VEP).
The output table contains the most severe predicted effect of the variant and the associated gene symbol. In addition, the minor allele frequency from the 1000 genomes project, frequency information from the Genome Aggregation Database (gnomAD), and the SIFT score are extracted (if available). The SIFT Score indicates whether an amino acid substitution affects protein function (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168916/), it ranges from 0 to 1, with low scores indicating a damaging effect. Those effects are calculated per transcript, therefore transcript information (Ensembl ID) is included as well.
In the interactive view the user can filter variants by minor allele frequencies and SIFT score and select variants of interest. If nothing is selected all data will be available at the output port. The view also contains an explanatory image of the variant consequences taken from http://www.ensembl.info/2012/08/06/variation-consequences/.

Input ports

1. Type: Table
   Input table with variants.

Output ports

1. Type: Table
   Output table containing the most severe consequence of the variant, variant frequencies from the 1000 genomes project and gnomAD, and the SIFT score.