Variant Effect Predictor
The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Simply input the coordinates of your variants and the nucleotide changes to find out the:
- genes affected by the variants
- location of the variants (e.g. upstream of a transcript, in coding sequence, in non-coding RNA, in regulatory regions)
- consequence your variants on the protein sequence (e.g. stop gained, missense, stop lost, frameshift)
- known variants that match yours, and the associated minor allele frequencies
- SIFT and PolyPhen scores for changes protein sequence
- ... And more!
How to access the Variant Effect Predictor
There are two ways to use the Variant Effect Predictor (VEP) for predicting functional consequences of known and unknown variants:
- web interface | Documentation | Launch web interface
- standalone perl script | Documentation | Download latest version
Use the web version if you have relatively small volumes of data or prefer to avoid command-line scripts. The script version is more flexible and allows processing of large volumes of data (it is written using the Ensembl perl API, and can be incorporated into your own code and extended).
The VEP was formerly known as the SNP Effect Predictor, and was published under this name. Please reference the following publication:
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F.
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.