Genetic variants that cause haploinsufficiency account for many autosomal dominant (AD) disorders. Gene-based diagnosis classifies variants that alter canonical splice signals as pathogenic, but due to imperfect understanding of RNA splice signals other variants that may create or eliminate splice sites are often clinically classified as variants of unknown significance (VUS). To improve recognition of pathogenic splice-altering variants in AD disorders, we used computational tools to prioritize VUS and developed a cell-based minigene splicing assay to confirm aberrant splicing. Using this two-step procedure we evaluated all rare variants in two AD cardiomyopathy genes, lamin A/C (LMNA) and myosin binding protein C (MYBPC3). We demonstrate that 13 LMNA and 35 MYBPC3 variants identified in cardiomyopathy patients alter RNA splicing, representing a 50% increase in the numbers of established damaging splice variants in these genes. Over half of these variants are annotated as VUS by clinical diagnostic laboratories. Familial analyses of one variant, a synonymous LMNA VUS, demonstrated segregation with cardiomyopathy affection status and altered cardiac LMNA splicing. Application of this strategy should improve diagnostic accuracy and variant classification in other haploinsufficient AD disorders.D NA sequence analysis of patient DNA has been used to clinically diagnose associated inherited diseases, leading to the identification of thousands of rare sequence variants in affected and unaffected individuals. Interpreting the medical significance of these variants has proven to be a significant challenge. The annotation of nonsense, frameshift, insertion, and deletion variants that cause a highly predictable outcome [i.e., loss of function (LoF) of proteins encoded by disease genes] allows these to be clinically classified as pathogenic variants in more than 4,000 genes that cause disease by haploinsufficiency (1). Classification of rare synonymous and missense variants in these genes, however, has been more difficult. Although bioinformatic algorithms predict that some variants may damage the encoded protein, these annotations are imperfect, and many rare variants remain unclassified and are clinically designated as variants of unknown significance (VUS) (2).Splicing signals reside at all exon-intron junctions and include a 9-bp 5′ splice donor sequence with an invariant GT dinucleotide and a 23-bp 3′ splice acceptor sequence with an invariant AG dinucleotide (3) (Fig. 1A). Variants that alter the canonical GT and AG dinucleotides in haploinsufficient autosomal dominant (AD) genes are diagnostically classified as pathogenic, whereas substitutions of the remaining seven residues within the donor sequence, or the 21 residues within the acceptor sequence, are often classified as VUS (4). VUS that alter these sequences, however, have the potential to disrupt normal RNA splicing (5) (resulting in donor or acceptor loss; Fig. 1C). Similarly, variants within a nearby intron or exon may sufficiently mimic the consensus donor...