ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.1380G>C (p.Thr460=) (rs145333518)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000123720 SCV000213313 likely benign Hereditary cancer-predisposing syndrome 2014-09-29 criteria provided, single submitter clinical testing
Color RCV000123720 SCV000681974 likely benign Hereditary cancer-predisposing syndrome 2015-09-22 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000211961 SCV000861180 likely benign not specified 2018-05-29 criteria provided, single submitter clinical testing
GeneDx RCV000211961 SCV000167063 benign not specified 2014-02-03 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Genetic Services Laboratory, University of Chicago RCV000211961 SCV000593477 likely benign not specified 2015-09-02 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589439 SCV000694182 likely benign not provided 2017-02-16 criteria provided, single submitter clinical testing Variant summary: The ATM c.1380G>C (p.Thr460Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide, which 4/5 splice prediction tools predict no significant impact on normal splicing and ESE finder predicts alterations to ESE binding. However, these predictions have yet to be confirmed by functional studies. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 23/121350 (1/5277), predominantly in the African cohort, 21/10404 (1/474), which exceeds the estimated maximal expected allele frequency for a pathogenic ATM variant of 1/999 for Breast Cancer. Therefore, suggesting this is likely a benign polymorphism found primarily in population(s) of African origin. The variant of interest has not been reported, to our knowledge, in affected individuals via publications. However, multiple clinical diagnostic laboratories classified this variant as benign. Taken together, this variant is classified as "likely benign."
Invitae RCV000196725 SCV000252597 benign Ataxia-telangiectasia syndrome 2018-01-09 criteria provided, single submitter clinical testing

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