This workflow illustrates a simple use of the Variant Effect Predictor verified component. The effect of genetic variants based on their genomic region is determined using Ensembl's Variant Effect Predictor (VEP) via their REST API (https://rest.ensembl.org/#VEP). The output table of the component 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. You can also find an application using this component in this blog post https://www.knime.com/blog/variant-prioritization-domain-expert-interaction and here on the KNIME hub: https://kni.me/w/xpPi0YzQ9jwpUC8N
Used extensions & nodes
Created with KNIME Analytics Platform version 4.3.0
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