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Variant Effect Predictor

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 and transcripts 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 of your variants on the protein sequence (e.g. stop gained, missense, stop lost, frameshift)
  • known variants that match yours, and associated minor allele frequencies from the 1000 Genomes Project
  • SIFT and PolyPhen scores for changes to protein sequence
  • ... And more!

Web interface

  • Point-and-click interface
  • Suits smaller volumes of data

Standalone perl script

  • More options, more flexibility
  • For large volumes of data

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.
Bioinformatics 26(16):2069-70(2010)
doi:10.1093/bioinformatics/btq330