Contribution of Noncanonical Splice Variants to TTN Truncating Variant Cardiomyopathy

Background: HeterozygousTTN truncating variants cause 10% to 20% of idiopathic dilated cardiomyopathy (DCM). Although variants which disrupt canonical splice signals (ie, invariant dinucleotide of the splice donor site, invariant dinucleotide of the splice acceptor site) at exon-intron junctions are readily recognized asTTN truncating variants, the effects of other nearby sequence variations on splicing and their contribution to disease is uncertain.Methods: Rare variants of unknown significance located in the splice regions of highly expressedTTN exons from 203 DCM cases, 3329 normal subjects, and clinical variant databases were identified. The effects of these variants on splicing were assessed using an in vitro splice assay.Results: Splice-altering variants of unknown significance were enriched in DCM cases over controls and present in 2% of DCM patients (P =0.002). Application of this method to clinical variant databases demonstrated 20% of similar variants of unknown significance inTTN splice regions affect splicing. Noncanonical splice-altering variants were most frequently located at position +5 of the donor site (P =4.4×107 ) and position -3 of the acceptor site (P =0.002). SpliceAI, an emerging in silico prediction tool, had a high positive predictive value (86%–95%) but poor sensitivity (15%–50%) for the detection of splice-altering variants. Alternate exons spliced out of mostTTN transcripts frequently lacked the consensus base at +5 donor and −3 acceptor positions.Conclusions: Noncanonical splice-altering variants inTTN explain 1-2% of DCM and offer a 10-20% increase in the diagnostic power ofTTN sequencing in this disease. These data suggest rules that may improve efforts to detect splice-altering variants in other genes and may explain the low percent splicing observed for many alternateTTN exons.