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Ensemble Variant Effect Predictor

Ensemble Variant Effect Predictor

Ensembl Variant Effect Predictor predicts the effects of single nucleotide polymorphism (SNPs), copy number variation (CNV), and indels on genes, transcripts, protein, and regulatory sequences.


Genetics; Genetic variation; Function analysis; Genomics


  • Operation: Protein modelling (mutation)
  • Input: A:
    1. chromosome - just the name or number, with no 'chr' prefix
    2. start
    3. end
    4. allele - pair of alleles separated by a '/', with the reference allele first
    5. strand - defined as + (forward) or - (reverse).
    6. identifier - this identifier will be used in VEP's output. If not provided, VEP will construct an identifier from the given coordinates and alleles.
    B:VCF; VCF - Structural variants; HGVS identifiers; Variant identifiers; Genomic SPDI notation; REST-style regions
  • Output: Uploaded variation; Location; Allele; Gene; Feature; Feature type; Consequence; Position in cDNA; Position in CDS; Position in protein; Amino acid change; Codon change; Co-located variation; Extra
  • Software interface: Command-line user interface; web user interface; Rest API
  • Language: Perl
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Apache License Version 2.0
  • Cost: Free
  • Version name: 97
  • Maturity: Mature
  • Credit: Wellcome Trust (grant numbers WT095908 and WT098051) and the European Molecular Biology Laboratory. This work has also received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement number 200754 (GEN2PHEN) and under grant agreement number 222664 (Quantomics), and from the European Union’s Horizon 2020 research and innovation programme under grant agreement number 634143 (MedBioinformatics).
  • Contact: wm2 _at_
  • Collection: EBI Tools


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PMID: 20439314
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McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R "Analysis Tool Web Services from the EMBL-EBI." Nucleic Acids Res. 2013 Jul;41(Web Server issue):W597-600.
PMID: 23671338
PMCID: PMC3692137

Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R "The EMBL-EBI bioinformatics web and programmatic tools framework." Nucleic Acids Res. 2015 Jul 1;43(W1):W580-4.
PMID: 25845596
PMCID: PMC4489272

Chojnacki S, Cowley A, Lee J, Foix A, Lopez R "Programmatic access to bioinformatics tools from EMBL-EBI update: 2017." Nucleic Acids Res. 2017 Jul 3;45(W1):W550-W553.
PMID: 28431173
PMCID: PMC5570243

Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, Basutkar P, Tivey ARN, Potter SC, Finn RD, Lopez R "The EMBL-EBI search and sequence analysis tools APIs in 2019." Nucleic Acids Res. 2019 Apr 12. pii: gkz268.
PMID: 30976793

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