Tandem splice acceptor sites: Profiling their relevance to human disease

Interpretation of variation, particularly the creation or disruption of tandem splice acceptor sites (NAGN_nAG variants), challenges genomic medicine practice.

We analyzed the creation and disruption of dinucleotide AG sites within ±30 bases of natural splice-acceptor sites in the GRCh37 human reference genome. These results were compared with variant data from the ClinVar and gnomAD databases, as well as with data from 779 National Institutes of Health Undiagnosed Diseases Program study participants. Using RNA sequencing, we assessed the splicing at NAGN_nAG variants for 107 of the Undiagnosed Diseases Program participants and compared the empirical data with SpliceAI predictions.

Creation or disruption of NAGN_nAG sites within 30 bases of the natural splice acceptor are enriched in ClinVar compared with gnomAD; however, such variants in the 2 databases are rarely differentiated by SpliceAI scores. Empirical evaluation via RNA sequencing analysis supported novel acceptor site usage from -21 to +30; splice-altering variants did not predominate in a specific region or have SpliceAI scores invariantly, suggesting increased spliceogenicity.

NAGN_nAG variants within 30 bp of the natural splice acceptor have a high probability of clinical relevance and are poorly contextualized for clinical utility. Their interpretation benefits from empirical evaluation via RNA analysis.