Genet Med. 2024 Sep 18:101276. doi: 10.1016/j.gim.2024.101276. Online ahead of print.
ABSTRACT
PURPOSE: To assess the differences in variant classifications using the ACMG/AMP 2015 guidelines and the Bayesian point-based classification system (here referred to as the point system) in 115 hereditary cancer predisposition genes and explore variant sub-tiering by the point system.
METHODS: Germline variant classifications for 721 pediatric patients from an in-house panel were retrospectively evaluated using the two scoring systems.
RESULTS: 2376 unique variants were identified, with ∼23.5% exhibiting discordant classifications. Unique variants classified by the point system demonstrated a lower rate of variants of uncertain significance (VUS; ∼15%) compared to ACMG/AMP 2015 (∼36%). This change is attributed to unique variants with one benign supporting evidence (∼12%) or one benign strong evidence (∼4%) being classified as likely benign by the point system. Additionally, variants with conflicting/modified evidence (∼5% of 2376) are also resolved by the point system. Sub-tiering unique variants classified by the point system as VUS (n=354) indicates ∼77.4% were VUS-Low (0-1 points), while the remaining ∼22.6% were VUS-Mid (2-3 points) and VUS-High (4-5 points).
CONCLUSION: The point system reduces the VUS rate and facilitates their sub-tiering. Future large-scale studies are warranted to explore the impact of the point system on improving VUS reporting and/or VUS clinical management.
PMID:39306722 | DOI:10.1016/j.gim.2024.101276
