Variant Predictors
SIFT
PolyPhen
REVEL
The rare exome variant ensemble learner (REVEL) method incorporates recently developed individual prediction tools as features and was trained on recently discovered disease and rare neutral missense variants that did not overlap with the training data for its constituent predictors. We also assembled two large independent test sets of recently discovered pathogenic and benign variants that parallel the likely application of REVEL to newly discovered variants from NGS studies. We benchmark the performance of REVEL and existing ensemble predictors for distinguishing disease mutations from neutral variants across a broad range of AFs. To make our method easily accessible for research and clinical use, we provide pre-computed REVEL scores for all possible human missense variants. (R1)
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. (R)
PhyloP
PhyloP (phylogenetic p-values) conservation scores are obtained from the PHAST package.
Based on Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes