Putative duplications overlapping the breast cancer tumour suppressor gene STK11 suggested decreased risk of breast cancer in our study for both BRCA1 carriers (HR = 0.49, 95%CI 0.29–0.81, p = 5.4 × 10−3) and BRCA2 carriers (HR = 0.44, 95%CI 0.22–0.88, p = 9.2 × 10−3). Here, STK11 is linked to cancer.