Introduction
Evaluating the potential functional impact of variants in Mendelian disease genes is a key component in the interpretation of their clinical significance. Disease gene databases chiefly contain nonsense, frameshift indels, and missense variants, in addition to variants that impact donor and acceptor splice site motifs. In particular, synonymous variants are often dismissed from variant curation and test reporting under the assumption that they are “silent” variants. However, these variants can still impact transcription, mRNA processing and translation (Sauna & Kimchi-Sarfaty, 2011). Further, intronic variants outside of the donor and acceptor splice site motifs are mostly disregarded in clinical testing and/or reporting due to the low sensitivity and specificity of currently available methods to predict their impact on mRNA splicing. This negative bias in recording of synonymous and intronic variants has implications for their inclusion in data analyses and functional studies in research settings.
Current variant interpretation approaches also generally ignore the fact that all types of exonic and intronic variants can potentially affect mRNA splicing (we will term these types of variants as being “spliceogenic”). Exonic variants initially annotated as synonymous, missense, nonsense or frameshift based on predicted codon usage can destroy, enhance or create motifs recognized by the mRNA splicing machinery (see below). Intronic variants outside the native splice sites can destroy branchpoint (BP) motifs, or create or enhance the use of cryptic sites. To improve assessment of variant pathogenicity and clinical decision-making, it is important to expand variant curation and reporting to include reliable bioinformatic prediction of spliceogenicity for variants located outside the donor and acceptor splice site motifs.