True somatic nonsense variants occurred in 6% of BLCA cases, affecting genes BRCA2, FANCM, FANCE, REV3L, and SLX4. Germline nonsense variants were predicted in 5% of BLCA cases, affecting BRCA2, FANCM, and FANCD2. Several of these germline variants showed potential loss of heterozygosity based on increased VAF in tumor DNA compared to germline DNA (Fig. 5b: FANCM R1931*, BRCA2 Y3308*). Here, SLX4 is linked to bladder transitional cell carcinoma.