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. (https://jmg.bmj.com/content/early/2023/01/01/jmg-2022-108931 )