Transcripts from Ensembl build (54) were used for annotation. Variants were classified into the following four Tiers.
Tier 1: All variants in the coding regions of annotated exons, canonical splice sites, and RNA genes.
Tier 2: All variants in conserved genomic regions (cutoff: conservation score greater than or equal to 500 based on either the phastConsElements28way table or the phastConsElements17way table from UCSC genome browser), and all variants in regulatory non-repeat masked regions annotated by UCSC annotation (Regulatory annotations included are targetScanS, ORegAnno, tfbsConsSites, vistaEnhancers, eponine, firstEF, L1 TAF1 Valid, Poly(A), switchDbTss, encodeUViennaRnaz, laminB1, cpgIslandExt).
Tier 3: Variants in non-repeat masked regions
Tier 4: All remaining SNVs
Transcripts from Ensembl build (67) were used for annotation. Variants were classified as outlined for build36 above, however, build37 UCSC tracks were only available for cpgIslandExt and repeatMasker regions. All other source UCSC tracks used were lifted over from build36.