ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.3517T>C (p.Leu1173=) (rs141460670)

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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 RCV000123742 SCV000213314 likely benign Hereditary cancer-predisposing syndrome 2014-09-29 criteria provided, single submitter clinical testing
Color RCV000123742 SCV000682135 likely benign Hereditary cancer-predisposing syndrome 2015-09-22 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000212000 SCV000861184 likely benign not specified 2018-05-29 criteria provided, single submitter clinical testing
GeneDx RCV000212000 SCV000167085 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 RCV000212000 SCV000593480 likely benign not specified 2015-09-02 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000212000 SCV000916610 benign not specified 2018-12-14 criteria provided, single submitter clinical testing Variant summary: ATM c.3517T>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 0.00022 in 277144 control chromosomes, predominantly at a frequency of 0.0023 within the African subpopulation in the gnomAD database. The observed variant frequency within African control individuals in the gnomAD database is approximately 2.3 fold of the estimated maximal expected allele frequency for a pathogenic variant in ATM causing Breast Cancer phenotype (0.001), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.3517T>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 (BRCA1 c.1386delG), providing supporting evidence for a benign role. Three 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/likely benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV000198270 SCV000252598 benign Ataxia-telangiectasia syndrome 2018-01-09 criteria provided, single submitter clinical testing

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