ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.4482T>C (p.Cys1494=) (rs769071554)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001081246 SCV000622505 likely benign Ataxia-telangiectasia syndrome 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000564304 SCV000660452 likely benign Hereditary cancer-predisposing syndrome 2017-05-17 criteria provided, single submitter clinical testing Synonymous alterations with insufficient evidence to classify as benign;In silico models in agreement (benign)
Color RCV000564304 SCV000687554 likely benign Hereditary cancer-predisposing syndrome 2017-01-03 criteria provided, single submitter clinical testing
GeneDx RCV000832613 SCV000974369 likely benign not provided 2018-06-18 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.
Integrated Genetics/Laboratory Corporation of America RCV001193041 SCV001361587 likely benign not specified 2019-01-30 criteria provided, single submitter clinical testing Variant summary: ATM c.4482T>C alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 1.6e-05 in 246118 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.4482T>C in individuals affected with Breast Cancer and no experimental evidence demonstrating its impact on protein function have been reported. Co-occurrences with other pathogenic variant(s) have been reported (BRCA2 c.5290_5291delTC, p.Ser1764fsX3), providing supporting evidence for a benign role. Three ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

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