ClinVar

Description

Variant summary: ATM c.4060C>A (p.Pro1354Thr) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00019 in 248752 control chromosomes, predominantly at a frequency of 0.0004 within the Non-Finnish European subpopulation in the gnomAD database. This frequency is not significantly higher than estimated for a pathogenic variant in ATM causing Breast Cancer (0.00019 vs 0.001), allowing no conclusion about variant significance. However, in certain European subpopulations the variant occurs with an even higher frequency, e.g. in Southern Europeans 0.0012 (14/11412 alleles), suggesting that the variant could be a benign polymorphism. In addition, the variant was reported in 6/7325 European American women, who were older than age 70, and have never had cancer (in the FLOSSIES database). c.4060C>A has been reported in the literature in individuals affected with Breast Cancer and other tumor phenotypes, but was also repeatedly found in controls or non-cancer-related patient cohorts (e.g. Tavtigian_2009, Bernstein_2010, Tavera-Tapia_2017, Tiao_2017, Quezada Urban_2018, Urbina-Jara_2019, Kraemer_2019, Fanale_2020, Dorling_2021, Guglielmi_2021, Yu_2022), providing no strong evidence for causality. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as VUS (n=9), likely benign (n=3)/benign (n=1). Based on the evidence outlined above, the variant was classified as likely benign.