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Background  Pathogenic variants (PVs) of BRCA genes entail a lifetime risk of developing breast cancer in 50–85% of carriers. Their prevalence in different populations has been previously reported. However, there is scarce information regarding the most common PVs of these genes in Latin-Americans. This study identified  BRCA1  and  BRCA2  PV frequency in a high-risk female population from Northeastern Mexico and determined the association of these mutations with the patients’ clinical and pathological characteristics.    Methods  Women were divided into three groups: aged ≤ 40 years at diagnosis and/or risk factors for hereditary breast cancer ( n  = 101), aged > 50 years with sporadic breast cancer ( n  = 22), and healthy women ( n  = 72) .  Their DNA was obtained from peripheral blood samples and the variants were examined by next-generation sequencing with Ion AmpliSeq  BRCA1  and  BRCA2  Panel using next-generation sequencing.    Results  PVs were detected in 13.8% group 1 patients ( BRCA1 , 12 patients;  BRCA2 , 2 patients). Only two patients in group 2 and none in group 3 exhibited  BRCA1  PVs. Variants of uncertain significance were reported in 15.8% patients ( n  = 16). In group 1, patients with the triple-negative subtype, PV frequency was 40% (12/30). Breast cancer prevalence in young women examined in this study was higher than that reported by the National Cancer Institute Surveillance, Epidemiology (15.5% vs. 5.5%, respectively).    Conclusions  The detected  BRCA1  and  BRCA2  PV frequency was similar to that reported in other populations. Our results indicate that clinical data should be evaluated before genetic testing and highly recommend genetic testing in patients with the triple-negative subtype and other clinical aspects.    Electronic supplementary material  The online version of this article (10.1186/s12885-019-5950-4) contains supplementary material, which is available to authorized users.

Analysis of the pathogenic variants of BRCA1 and BRCA2 using next-generation sequencing in women with familial breast cancer: a case–control study