Exonic variants can lead to loss/gain of SREs
Variants annotated as synonymous, missense, nonsense, or frameshift variants that disrupt exonic SREs have been identified in hereditary cancer genes. Most of the published splicing assays on exonic SREs have focused on variants in BRCA1, BRCA2 and the mismatch repair genes (MLH1 , MSH2 , MSH6 and PMS2 ). We have generated a comprehensive list of 81 variants in exonic SREs in these genes that resulted in exon skipping in Supplementary Table 1 (BRCA1 , BRCA2 ) and Supplementary Table 2 (MLH1 ,MSH2 , MSH6 , PMS2 ). Exonic splicing variants in other hereditary cancer genes include: a synonymous variant in theAPC gene, NM_000038.6:c.1869G>T [p.(Arg623=)], detected in a familial adenomatous polyposis family, that leads to exon 14 skipping (Montera et al., 2001); and two nonsense NF1 variants identified in Neurofibromatosis type 1 patients, NM_000267.3:c.6792C>A and NM_000267.3:c.6792C>G [both initially annotated as p.(Tyr2264*)] that induce skipping of exon 37 and exons 36-37 (Baralle et al., 2006; Messiaen, Callens, De Paepe, Craen, & Mortier, 1997). In addition to single nucleotide substitutions, other types of exonic variants can also disrupt SREs, such as small deletions, e.g. NM_000059.3(BRCA2 ):c.470_474del (Sanz et al., 2010), and duplications, e.g. NM_000535.6(PMS2 ):c.325dup (van der Klift et al., 2015). Some variants can act through a combination of mechanisms. For example, NM_000249.3(MLH1 ):c.840T>A [p.(Tyr280*)] and NM_000249.3(MLH1 ):c.842C>T [p.(Ala281Val)] have each been shown to disrupt an SRE and at the same time create a new donor site leading to exon skipping and partial exon deletion (Soukarieh et al., 2016).