BAP1 and nonpapillary renal cell carcinoma: To evaluate the prognostic values of the frequently mutated genes or SCNAs, we performed Kaplan–Meier analysis of the somatic alterations and identified 18 somatic events (including del(9), amp(12), del(14q), del(1p), del(4), del(13q), amp(3q), del(11q), del(22q), del(15q), del(2q), and mutations in genes VHL and BAP1) as potential factors relevant to the prognosis of ccRCC (Supplementary Data 3).