Aberrant splicing prediction during human organ development

Developmental disorders constitute a major class of genetic diseases, yet tools to identify splicing-disruptive variants during development are lacking. To address this need we extended the AbSplice framework to incorporate splicing dynamics across developmental stages. Moreover, we introduced several improvements including a refined ground truth from the aberrant splicing caller FRASER2, a continuous representation of splice site usage, and integration of the rich set of predictions from the sequence-based model Pangolin. These advances double the precision and recall of the original model at predicting aberrant splicing events and enable predictions across embryonic, childhood, and adult tissues. Genome-wide scores for all single-nucleotide variants and a web interface to score indels are available to facilitate the exploration of the predictions. Our genome-wide predictions reveal a class of variants with splicing-disruptive effects confined to early development, particularly abundant in the brain (>18,000 variants). Analysis of genomes of individuals with a suspected Mendelian disorder from Genomics England’s National Genomics Research Library identified 26 unique variants in disease-linked genes, with stronger predicted effects during development than in adulthood, including a candidate new diagnosis in the gene FGFR1 . Altogether, these results improve the accuracy of splice-disruptive variant prediction and provide developmental context to aid interpretation.