PheWAS forest plot for all-site cancers using SGE-depleted variants and controls; regression model effect is shown by data points and effect standard error is shown by bars (Supplementary Table 7 ). Rare variant burden test masks (and CADD, EVE and REVEL 56 predictors) are shown by color for BAP1 variants in UK Biobank ( n carriers shown in key). Significance, according to the corrected P value determined by generalized linear modeling (Supplementary Method 14 ), is indicated by a triangle (significant) or a circle (not significant). SGE-depleted nonsynonymous variants (yellow) showed a significant effect and are therefore associated with increased cancer risk. SGE-depleted high-confidence (HC) protein-truncating variants (PTVs; orange) demonstrated a significant effect, as did HC PTVs (red).
