ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.3342G>A (p.Lys1114=) (rs138393322)

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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 RCV000123738 SCV000213227 likely benign Hereditary cancer-predisposing syndrome 2014-07-18 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000586815 SCV000840933 benign not provided 2018-06-08 criteria provided, single submitter clinical testing
Color RCV000123738 SCV000682121 benign Hereditary cancer-predisposing syndrome 2015-02-13 criteria provided, single submitter clinical testing
GeneDx RCV000211997 SCV000167081 benign not specified 2013-12-11 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 RCV000586815 SCV000694258 likely benign not provided 2017-01-03 criteria provided, single submitter clinical testing Variant summary: The ATM c.3342G>A (p.Lys1114Lys) variant causes a synonymous change involving a non-conserved nucleotide, which 3/5 Alamut algorithms predict an alteration to a cryptic splice acceptor site and ESE finder predicts alterations to ESE binding, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 59/118068 (1/2001), which does not exceed the estimated maximal expected allele frequency for a pathogenic ATM variant for Atxia-Telengiectasia 1/252 or Breast Cancer 1/1999. The variant was identified in one breast cancer patient without evidence of causality; and the allele frequency in the European non-Finnish ExAC subpopulation (54/64684; 0.000834828), is higher than the estimated maximal expected allele frequency of a pathogenic ATM variant for Breast Cancer (0.0005001), suggesting this variant is not associated with breast cancer. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as Likely Benign, without evidence to independently evaluate. Furthermore, an internal LCA sample reports the variant to co-occur with a pathogenic BRCA2 variant, c.5946delT (p.S1982fsX22). Taken together, this variant is classified as "Likely Benign."
Invitae RCV000122842 SCV000166100 benign Ataxia-telangiectasia syndrome 2018-01-15 criteria provided, single submitter clinical testing
PreventionGenetics RCV000586815 SCV000805538 likely benign not provided 2016-10-03 criteria provided, single submitter clinical testing

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