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Table 4 Examples of VEP plugins

From: The Ensembl Variant Effect Predictor

Plugin Maintained by Functionality
CADD Martin Kircher Integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations
dbNSFP Ensembl Provides pre-calculated scores from dbNSFP for many pathogenicity prediction tools for every possible missense variant in the human genome [96]
dbscSNV Ensembl Retrieves data for splice variants from dbscSNV [97]
ExAC Ensembl Retrieves ExAC allele frequencies from the Exome Aggregation Consortium (ExAC) project [32]
GWAVA Graham Ritchie Predicts the functional impact of variants on non-coding elements from, e.g., ENCODE using GWAVA
GXA Ensembl Reports data from the Expression Atlas
LD Ensembl Finds variants in linkage disequilibrium with any overlapping existing variants
LOFTEE Konrad Karczewski Predicts if stop gain, splice site, or frameshift variants lead to loss of function (LoF) in the affected protein
MaxEntScan Ensembl Compares scores for reference and mutant splice site sequences using a maximum entropy method
miRNA Ensembl Reports whether a variant is predicted to fall in a stem or loop region of a mature miRNA
UpDownStream Ensembl By default the VEP searches 5 kb either side of input variants for transcripts. Configures this distance which is useful in species with small intergenic distances or for investigating long-range trans-acting regulatory interactions
VAX Michael Yourshaw Incorporates data from KEGG, Human Protein Atlas, MitoCarta, OMIM, and more into VEP output
  1. For a full list of plugins see [76]