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Ensembl Variant Effect Predictor (VEP)

Ensembl Variant Effect Predictor (Ensembl VEP)

Ensembl VEP predicts the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on gene transcripts and protein sequence, as well as regulatory regions. It reports reference data including gene and variant phenotype associations and population allele frequencies to facilitate variant prioritisation and interpretation.

Simply input the coordinates of your variants and the nucleotide changes to find out the:
  • Genes and Transcripts overlapping the variant, which it may impact
  • Predicted consequence of your variants on the protein (e.g. stop gained, missense,, frameshift), transcript ( e.g. splice_donor_variant) or regulatory element ( e.g. regulatory_region_variant, TF_binding_site_variant) see variant consequences
  • Known variants that match yours, and associated allele frequencies from projects including gnomAD and the 1000 Genomes Project, citation and links to information in other resources
  • Predictions of variant deleteriousness from tools including AlphaMissense, CADD, SIFT, REVEL and SpliceAI
  • Functional assay results from sources including MaveDB
  • ... And more! See the current analysis options, data versions.

What's new in release 114?


Ensembl 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 Ensembl VEP, please cite our most recent publication to help us continue to support 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


tools related to Ensembl VEP

Variant recoder

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

Command line:

Clone from GitHub| Download (zip)

REST API:

Variant Recoder REST API

Haplosaurus

Computes observed transcript haplotype sequences based on phased genotype data

Command line:

Clone from GitHub| Download (zip)

REST API:

Haplosaurus REST API