Variant reclassification in cancer susceptibility genes and an updated variant spectrum of Turkish breast and colorectal cancer patients.

Multigene panel testing (MGPT) is a powerful tool for identifying pathogenic variants (PVs) underlying hereditary cancers. However, the clinical interpretation of variants of uncertain significance (VUS) remains a major challenge, particularly in populations underrepresented in population genomic databases. In this study, we analyzed 25 cancer susceptibility genes in a Turkish cohort comprising 1293 breast cancer (BC) patients, 370 colorectal cancer (CRC) patients, and 914 cancer-free controls. Compared with our previous work, the expanded dataset enabled a more refined classification of germline variants. In total, we identified 217 distinct PVs and 494 distinct VUS. Among BC patients, PVs were enriched in BRCA1, BRCA2, PALB2, CHEK2, and ATM, while in CRC patients PVs were enriched in MLH1, MUTYH, MSH2, and CHEK2. Notably, CHEK2 was among the most frequently mutated genes, and harbored the highest number of distinct PVs and VUS per coding region. Given the underrepresentation of the Turkish population in public variant databases and the continuous accumulation of population and functional evidence, we systematically re-evaluated the 415 VUS reported 5 years ago in the initial freeze of this cohort. This reclassification resulted in 98 VUS being reclassified as benign and 16 as PVs, increasing positive test rates by 3.7% in BC patients and 1.6% in CRC patients, while reducing inconclusive results by approximately 9% across all study groups. Overall, this study underscores the importance of case–control design for population-specific variant interpretation and demonstrates how systematic reclassification can substantially enhance the clinical utility of MGPT. The findings contribute to improving hereditary cancer risk prediction in the Turkish population and have important implications for the development of future variant reclassification frameworks.