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Version: 3.23

REVEL

Overview

REVEL is an ensemble method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons.

Publication

Ioannidis, N. M. et al. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. The American Journal of Human Genetics 99, 877-885 (2016). https://doi.org/10.1016/j.ajhg.2016.08.016

CSV File

Example

chr,hg19_pos,grch38_pos,ref,alt,aaref,aaalt,REVEL
1,35142,35142,G,A,T,M,0.027
1,35142,35142,G,C,T,R,0.035
1,35142,35142,G,T,T,K,0.043
1,35143,35143,T,A,T,S,0.018
1,35143,35143,T,C,T,A,0.034

Parsing

From the CSV file, we're mainly interested in the following columns:

  • chr
  • hg19_pos
  • grch38_pos
  • ref
  • alt
  • REVEL

Known Issues

Sorting

Since the input file contains positions for both GRCh37 and GRCh38, we split it into two TSV files (for the sake of better readability) with identical format. The positions for GRCh37 were sorted but not for GRCh38. So we re-sort the variants by position in the GRCh38 file.

Conflicting Scores

When there are multiple scores available for the same variant (i.e. the same position with the same alternative allele), we pick the highest score.

Download URL

https://sites.google.com/site/revelgenomics/downloads

JSON Output

"revel":{ 
   "score":0.027
}
FieldTypeNotes
scorefloatRange: 0 - 1.0