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Variant Effect Predictor (VEP)

BioCodeKb - Bioinformatics Knowledgebase

The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs. It determines the effect of our variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Analysis of variant data resulting from genome or exone sequencing is necessary for progress in biology, from basic research to translational genomics in the clinic. It is key for investigating function and for progressing from a system of medical care based on standardized treatment to one targeted to the individual patient.


  • The VEP has been used for analysis of traits in farm animals

  • for patient diagnosis in the clinic

  • for research on GWAS

  • used for analysis in many large-scale projects, including the 1000 Genomes and Exome Aggregation Consortium (ExAC)

  • Find out the genes and transcripts affected by the variants

  • Know the location of the variants (e.g. upstream of a transcript, in coding sequence, in non-coding RNA, in regulatory regions)

  • Consequence of our variants on the protein sequence (e.g. stop gained, missense, stop lost, frameshift)

  • Known variants that match ours, and associated minor allele frequencies from the 1000 Genomes Project

VEP’s annotations are used as input to tools for deep exploration of variant annotation such as GEMINI.

The VEP annotates two broad categories of genomic variant;

  1. sequence variants with specific and well-defined changes

  2. Larger structural variants (greater than 50 nucleotides in length), including those with changes in copy number or insertions and deletions of DNA.

We can input coordinates of any alleles we have identified or variant identifiers. A full list of input files is available. If a variant that we enter as input causes a change in the protein sequence, the VEP will calculate the possible amino acids at that position and the variant would be given a consequence type of missense. Download our results in multiple data formats, easily share our results with others, and integrate our variation data with the powerful Ensembl web browser.

We have three options for uploading our data:

  1. File upload

  2. Paste file

  3. File URL - point the VEP to a file hosted on a publically accessible adderess

The summary panel on the VEP results page gives a brief overview of the VEP job, with some basic statistics about the results.

Statistics include;

  1. Variants processed

  2. Variants remaining after filtering

  3. Novel / known variants

  4. Number of overlapped genes, transcripts and regulatory features

  5. Pie charts are shown detailing the proportion of consequence types called across all variants in the results


Need to learn more about Variant Effect Predictor (VEP) and much more?

To learn Bioinformatics, analysis, tools, biological databases, Computational Biology, Bioinformatics Programming in Python & R through interactive video courses and tutorials, Join BioCode.

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