USP9X and cancer: We observe a significant overrepresentation of nc-SCMs in cancer genes, including NFE2L2, CDKN2B, FUBP1, MAP2K2, TBX3, FCGR3A, SETD2, DNER, ETV6, USP9X, MAP4K3, MDM2, and STK11 (p < 0.001); see “Methods.” CSPP1, STK11, SLCO1B1, NSMCE4A, and MAP4K3 contain two splice-creating mutations each, most of which have a DNA VAF and RNA JAF >20%.