A large fraction of disease causing DNA variants are known to disrupt mRNA structure or expression. Whereas, long-read RNA sequencing is a powerful tool to assess mRNA structure, its sensitivity is limited. Here, we developed CAPLRseq as an adaptable workflow for effective transcriptome-based disease diagnosis. CAPLRseq can evaluate a wide range of simple and complex DNA variants that affect mRNA structure. We validated CAPLRseq for the diagnosis of Lynch Syndrome, a hereditary cancer predisposition syndrome. The method may be incorporated into the diagnostic workflow to unambiguously classify DNA variants of uncertain significance in hereditary cancer predisposition genes. (By Dr. med. Dieter Wolf, https://jmg.bmj.com/content/early/2023/01/01/jmg-2022-108931 )