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Ensembl Variant Effect Predictor (VEP)

Ensembl Variant Effect Predictor (VEP)


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-2 scores for changes to protein sequence
  • ... And more! See data types, versions.

VEP interfaces

Web interface

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

Command line tool

  • More options and flexibility
  • For large volumes of data

REST API

  • Language-independent API
  • Simple URL-based queries


Publication

If you use VEP, please cite our UPDATED publication so we can continue to support VEP development:

Cite us

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F.
The Ensembl Variant Effect Predictor.
Genome Biology Jun 6;17(1):122. (2016)
doi:10.1186/s13059-016-0974-4



VEP related tools

Variant recoder

Translate a variant identifier or HGVS notation to all possible variant IDs and HGVS

Haplosaurus

Computes observed transcript haplotype sequences based on phased genotype data

Command line (VEP):

Clone from GitHub| Download (zip)

REST API:

Haplosaurus REST API