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Variant Effect Predictor (VEP)

Definition
AI-generated

VEP is the Ensembl Variant Effect Predictor, a software tool for annotating genetic variants with predicted consequences on transcripts, proteins, regulatory features, and known identifiers.

Topics
Post-GWAS
URL
https://www.ensembl.org/info/docs/tools/vep/index.html
Related
ANNOVAR Canonical Transcript Ensembl

Why it matters in GWAS

VEP is one of the standard tools for post-GWAS interpretation of lead and fine-mapped variants. Consequence labels depend on genome build, transcript set, and configuration, so VEP settings are part of the reproducibility details for downstream biological interpretation.

Example usage

"Lead variants were annotated with VEP on GRCh38 using GENCODE transcripts to flag predicted protein-altering effects."

ANNOVAR Canonical Transcript Ensembl GENCODE RefSeq Variant Annotation
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • McLaren W, et al. (2016). The Ensembl Variant Effect Predictor. Genome Biol. https://doi.org/10.1186/s13059-016-0974-4
  • GWASTutorial: Annotation by ANNOVAR & VEP.
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