S1 Gene HGNC symbol TranscriptEnsemblv65 ENST ID from version 65 P900 Proportion of transcript with coverage >=15x in 900+ individuals P500 Proportion of transcript with coverage >=15x in 500+ individuals PercentTargeted Proportion of transcript targeted by Illumina TruSeq Exome CodingLength Length of coding sequence in bp, from start to stop codon Chromosome Chromosome that gene occurs on cDNAStart hg19 coordinate of c.1 in the transcript cDNAStop hg19 coordinate of last c. base in the transcript Exclusion Reason for exclusion from variant analysis VariationType Type of variation present in gene S2 CHR Chromosome POS hg19 position REF Reference allele ALT Alternate allele GENE HGNC symbol, separated by ":" when present in overlapping genes CSN most 3' annotation from CAVA according to chosen transcript in S1 CLASS class from CAVA's ontology TRANS selected ENST ID, separated by ":" when present in overlapping genes LOC affected exon Type type of variant - bs for base substitution, ins for insertion, del for deletion AlternateAnnotation can an indel be represented differently based on sequence context; HGVSNotClass if change is in HGVS alone, HGVSAndClass if change affects class ontology IDLength length of indel VarFreq frequency of variant in control series MostSevere most severe class from CAVA's ontology GenePosition position of protein-truncating variant (PTV) in coding length of gene FType frequency type of variant PTV 1 if most severe effect is a PTV, 0 otherwise PTVStringent 1 if most severe effect is PTV occurring in the first 95% of the transcript, 0 otherwise controlhom number of high confidence homozygous calls controlhet number of high confidence heterozygous calls controlmulti number of multi-allelic calls with this variant LQHom number of lower confidence homozygous calls LQHet number of lower confidence heterozygous calls dbSNP138 rsID from dbSNP138 for base substitutions EMAF MAF from Exome Variant Server European-American individuals for base substitutions AMAF MAF from Exome Variant Server African-American individuals for base substitutions ETotalIndiv number of Exome Variant Server European-American individuals corresponding to EMAF ATotalIndiv number of Exome Variant Server African-American individuals corresponding to AMAF TRINFO strand of transcript, total length of transcript, number of exons, and coding length of transcript separated by "/"" IMPACT predicted impact from CAVA ALTANN alternative most 5' annotation from CAVA according to chosen transcript in S1 ALTCLASS alternative most 5' class from CAVA's ontology