Resolving non‑coding splice‑altering variants using an integrative genomic and transcriptomic workflow: application to FOXP1

Genome sequencing (GS) often reveals non-coding variants of uncertain significance, especially those predicted to affect pre-mRNA splicing. We present an integrative workflow combining splice prediction, a minigene assay and long-read RNA sequencing to assess their functional impact. Applied to a de novo heterozygous 17-bp intronic deletion in FOXP1 from a child with a neurodevelopmental disorder, this approach showed impaired exon recognition and multiple aberrant transcript isoforms, supporting a loss-of-function mechanism consistent with FOXP1 haploinsufficiency. Our results illustrate how experimental and isoform-resolved transcriptomic analyses can refine the interpretation of non-coding splice-altering variants detected by GS in clinical genomics.