The Ensembl Variant Effect Predictor

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2016 Jun 9

PMID 27268795

Citations 3666

Authors

William McLaren

Laurent Gil

Sarah E Hunt

Harpreet Singh Riat

Graham R S Ritchie

Anja Thormann

Paul Flicek

Fiona Cunningham

Affiliations

Soon will be listed here.

Abstract

The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.

Citing Articles

Clinical and molecular spectrum of TK2-deficiency: a large Brazilian cohort.

Moreno C, Artilheiro M, Fonseca A, da Silva A, Fernandes T, Camelo C Sci Rep. 2025; 15(1):9013.

PMID: 40089535 DOI: 10.1038/s41598-024-84373-5.

Mutational constraint analysis workflow for overlapping short open reading frames and genomic neighbors.

Danner M, Begemann M, Kraft F, Elbracht M, Kurth I, Krause J BMC Genomics. 2025; 26(1):254.

PMID: 40087590 DOI: 10.1186/s12864-025-11444-w.

Exome sequencing shows same pattern of clonal tumor mutational burden, intratumor heterogenicity and clonal neoantigen between autologous tumor and Vigil product.

Willoughby D, Bognar E, Stanbery L, Nagel C, Wallraven G, Pruthi A Sci Rep. 2025; 15(1):8637.

PMID: 40082566 PMC: 11906592. DOI: 10.1038/s41598-025-90136-7.

PON-P3: Accurate Prediction of Pathogenicity of Amino Acid Substitutions.

Kabir M, Ahmed S, Zhang H, Rodriguez-Rodriguez I, Najibi S, Vihinen M Int J Mol Sci. 2025; 26(5).

PMID: 40076632 PMC: 11899954. DOI: 10.3390/ijms26052004.

Chromosomal Location and Identification of as a New Gene Responsible for Familial Bicuspid Aortic Valve.

Li Y, Zou S, Bian Y, Liu X, Yang C, Li L Diagnostics (Basel). 2025; 15(5).

PMID: 40075846 PMC: 11898536. DOI: 10.3390/diagnostics15050600.

References

Liu X, Jian X, Boerwinkle E . dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat. 2013; 34(9):E2393-402. PMC: 4109890. DOI: 10.1002/humu.22376. View

Rodriguez J, Maietta P, Ezkurdia I, Pietrelli A, Wesselink J, Lopez G . APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res. 2012; 41(Database issue):D110-7. PMC: 3531113. DOI: 10.1093/nar/gks1058. View

Stenson P, Ball E, Mort M, Phillips A, Shaw K, Cooper D . The Human Gene Mutation Database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution. Curr Protoc Bioinformatics. 2012; Chapter 1:1.13.1-1.13.20. DOI: 10.1002/0471250953.bi0113s39. View

Hindorff L, Sethupathy P, Junkins H, Ramos E, Mehta J, Collins F . Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009; 106(23):9362-7. PMC: 2687147. DOI: 10.1073/pnas.0903103106. View

Saunders C, Miller N, Soden S, Dinwiddie D, Noll A, Alnadi N . Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med. 2012; 4(154):154ra135. PMC: 4283791. DOI: 10.1126/scitranslmed.3004041. View

Adams D, Altucci L, Antonarakis S, Ballesteros J, Beck S, Bird A . BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol. 2012; 30(3):224-6. DOI: 10.1038/nbt.2153. View

Paila U, Chapman B, Kirchner R, Quinlan A . GEMINI: integrative exploration of genetic variation and genome annotations. PLoS Comput Biol. 2013; 9(7):e1003153. PMC: 3715403. DOI: 10.1371/journal.pcbi.1003153. View

Pedersen B, Layer R, Quinlan A . Vcfanno: fast, flexible annotation of genetic variants. Genome Biol. 2016; 17(1):118. PMC: 4888505. DOI: 10.1186/s13059-016-0973-5. View

Shihab H, Gough J, Cooper D, Stenson P, Barker G, Edwards K . Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat. 2012; 34(1):57-65. PMC: 3558800. DOI: 10.1002/humu.22225. View

10.

Petryszak R, Burdett T, Fiorelli B, Fonseca N, Gonzalez-Porta M, Hastings E . Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res. 2013; 42(Database issue):D926-32. PMC: 3964963. DOI: 10.1093/nar/gkt1270. View

11.

Landrum M, Lee J, Riley G, Jang W, Rubinstein W, Church D . ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2013; 42(Database issue):D980-5. PMC: 3965032. DOI: 10.1093/nar/gkt1113. View

12.

Abecasis G, Auton A, Brooks L, DePristo M, Durbin R, Handsaker R . An integrated map of genetic variation from 1,092 human genomes. Nature. 2012; 491(7422):56-65. PMC: 3498066. DOI: 10.1038/nature11632. View

13.

Gonzalez-Perez A, Deu-Pons J, Lopez-Bigas N . Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. Genome Med. 2012; 4(11):89. PMC: 4064314. DOI: 10.1186/gm390. View

14.

Gudbjartsson D, Helgason H, Gudjonsson S, Zink F, Oddson A, Gylfason A . Large-scale whole-genome sequencing of the Icelandic population. Nat Genet. 2015; 47(5):435-44. DOI: 10.1038/ng.3247. View

15.

Gonzalez-Perez A, Mustonen V, Reva B, Ritchie G, Creixell P, Karchin R . Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013; 10(8):723-9. PMC: 3919555. DOI: 10.1038/nmeth.2562. View

16.

Daetwyler H, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brondum R . Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet. 2014; 46(8):858-65. DOI: 10.1038/ng.3034. View

17.

Leslie E, Taub M, Liu H, Steinberg K, Koboldt D, Zhang Q . Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. Am J Hum Genet. 2015; 96(3):397-411. PMC: 4375420. DOI: 10.1016/j.ajhg.2015.01.004. View

18.

Gonzaga-Jauregui C, Lupski J, Gibbs R . Human genome sequencing in health and disease. Annu Rev Med. 2012; 63:35-61. PMC: 3656720. DOI: 10.1146/annurev-med-051010-162644. View

19.

Cooper G, Stone E, Asimenos G, Green E, Batzoglou S, Sidow A . Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005; 15(7):901-13. PMC: 1172034. DOI: 10.1101/gr.3577405. View

20.

Schwarz J, Cooper D, Schuelke M, Seelow D . MutationTaster2: mutation prediction for the deep-sequencing age. Nat Methods. 2014; 11(4):361-2. DOI: 10.1038/nmeth.2890. View