In patient BC228, who was diagnosed with an embryonal rhabdomyosarcoma on the basis of ovarian teratoma and carried germline pathogenic variant in DICER1, we also identified a 4.6 Mb large de novo deletion on 13q encompassing the genes BRCA2 and NBEA. The deletion likely explains the patient’s intellectual disability and confers increased risk for breast and ovarian cancer in adulthood. Here, BRCA2 is linked to embryonal rhabdomyosarcoma.