Impact of germline panel size on hereditary cancer: findings of variants of uncertain significance in the Brazilian public health population selected for high hereditary cancer risk

Introduction Breast cancer is the most common malignant neoplasm among women in Brazil, excluding non-melanoma skin cancers, with a significant proportion of hereditary cases associated with pathogenic or likely pathogenic germline variants (PV/LPV) in various genes. The increased use of multigene panels to identify these PV/LPV has been recommended but highlights the challenge of detecting variants of uncertain significance (VUS), which complicate genetic counseling and clinical management. Objective To evaluate epidemiological and reproductive aspects, as well as the size of different germline multigene panels that may influence the proportion of VUS detections. Materials and methods A cross-sectional study was conducted with rigorous inclusion criteria, encompassing women with personal or family history relevant to hereditary breast cancer from November 2021 to October 2022 at the High-Risk Outpatient Clinic, of the Women's Hospital Prof. José Aristodemo Pinotti—CAISM, University of Campinas (UNICAMP). Selection was based on the NCCN 2022 criteria. Samples were analyzed using next-generation sequencing (NGS), focusing on 144 genes associated with hereditary syndromes. The following statistical tests were applied: Chi-Square, Fisher's Exact, Kruskal–Wallis, Bowker, McNemar, and Stepwise logistic regression. Significance level was set at p < 0.05. Results Among the 364 patients analyzed, 51 (14%) presented benign or likely benign results, while 313 (86%) showed alterations, including VUS and PV/LPV. The prevalence of VUS was high, particularly in the ATM gene. Univariate and multivariate logistic regression analyses detected no associations between the presence of VUS and reproductive or epidemiological variables. The 144-gene panel identified a higher number of VUS compared to the 20- or 23-gene panels: 56.3 vs. 23.9, and 31%, respectively ( p < 0.001; p < 0.001). Conclusion The findings underscore the importance of panel size in the identification of PV/LPV vs. VUS. Most patients presented VUS, with the ATM gene being the most affected. None of the reproductive or epidemiological variables studied were associated with the presence of VUS across all groups. While the extended 144-gene panel significantly increased the detection of VUS compared to smaller panels (20–23 genes), it did not substantially improve the identification rate of PV/LPV, highlighting the need to improve genetic panels, especially for genetically diverse populations like the Brazilian population.