There was modest evidence of an association with overall breast cancer risk for rare missense variants (Table 2) in three genes: TMEM161A (OR = 2.56 (CI 95% 1.19–5.51), p-value = 0.016), SIPA1L1 (OR = 1.68 (CI 95% 1.06–2.67), p-value = 0.026), and ERCC2 (OR = 1.45 (CI 95% 1.01–2.08), p-value = 0.047). Here, SIPA1L1 is linked to breast carcinoma.