ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.2967T>C (p.Thr989=) (rs144145128)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000420259 SCV000512151 benign not specified 2015-09-21 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.
Ambry Genetics RCV000562520 SCV000660546 likely benign Hereditary cancer-predisposing syndrome 2016-02-26 criteria provided, single submitter clinical testing Synonymous alterations with insufficient evidence to classify as benign
Color RCV000562520 SCV000682095 likely benign Hereditary cancer-predisposing syndrome 2015-12-08 criteria provided, single submitter clinical testing
Invitae RCV000628300 SCV000749196 likely benign Ataxia-telangiectasia syndrome 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000420259 SCV001361586 likely benign not specified 2019-01-29 criteria provided, single submitter clinical testing Variant summary: ATM c.2967T>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 1.4e-05 in 277100 control chromosomes in the gnomAD database (exclusively found in the African subpopulation). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. In addition, the variant was also reported in 3 / 2559 African American women (i.e. with a frequency of 0.0012), who were older than 70 years of age, and never had cancer (in the FLOSSIES database). To our knowledge, no occurrence of c.2967T>C in individuals affected with Ataxia-Telangiectasia and no experimental evidence demonstrating its impact on protein function have been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign (1x) / likely benign (3x). Based on the evidence outlined above, the variant was classified as likely benign.

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