Fig. 1

Overview of the regional splicing constraint model. A The per-site splicing substitution rate by reference allele and Sum SpliceAI score bin across autosomal protein-coding genes. The rate of no substitutions across all SpliceAI score bins for each reference allele is A > A = 0.9003, C > C = 0.8565, G > G = 0.8433, and T > T = 0.9347 B Calculating an Observed over Expected (O/E) ratio for a genomic region by counting the number of variants in that region from gnomAD and the number of expected variants with a given SpliceAI score. C The O/E score distribution. Smaller O/E scores indicate higher constraint against splicing, while larger O/E scores indicate lower constraints against splicing. (O/E plot truncated at -2000 to 2000 for visibility) D Representation of regional splicing constraint O/E scores across a hypothetical gene. The presence of gnomAD variants, in gray and the SpliceAI prediction for each position in the gene, in shades of red influences the splicing-specific observed and expected counts in a region. gnomAD variants with higher SpliceAI scores show evidence for more tolerance against splicing variation. In contrast, sites with a higher SpliceAI score and no gnomAD variant show evidence for less tolerance against splicing. Pathogenic splicing variants, in black, are commonly absent from gnomAD and have predictions of alternative splicing from SpliceAI. In this example, the regional constraint model identifies constraint signals at regions that harbor pathogenic splicing variants, such as at canonical splice regions (^) and cryptic splice regions (^^). All genomic positions in C without a SpliceAI score should be recognized as sites with a SpliceAI score < 0.1