Table 1

Selected annotation tasks from the wANNOVAR server

Gene annotationVariant functionExonic, intronic, intergenic, UTR, etc
GeneImpacted gene or neighbouring gene (with distance)
Exonic variant functionNon-synonymous, synonymous, stopgain, etc
AAChangemRNA and amino acid change for coding variants
Variation databasesESP5400_ALLAllele frequency in 5400 NHLBI-ESP exomes
1000G_ALLAllele frequency in 1000 Genomes Project (currently, version 2012 Feb)
dbSNPdbSNP identifier (currently, version 135)
Functional predictionAVSIFTBase-level SIFT scores
LJB_SIFT1-SIFT scores and predictions (D: damaging, T: tolerated)
LJB_PolyPhen2PolyPhen 2 scores and predictions (D: probably damaging; P: possibly damaging; B: bening)
LJB_LRTLRT scores and predictions (D: deleterious; N: neutral; U: unknown)
LJB_MutationTasterMutationTaster scores and predictions (A: disease_causing_automatic; D: disease_causing; N: polymorphism; P: polymorphism_automatic)
LJB_PhyloPPhyloP conservation scores and predictions (C: conserved, N: non-conserved)
GERP++GERP++ scores for exonic variants
Region annotationConservedRegion-level phastCons LOD scores
SegDupLocated in segmental duplication region and the sequence identity score