ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.4980C>T (p.Asn1660=)

gnomAD frequency: 0.00019  dbSNP: rs144338238
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Total submissions: 17
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001084181 SCV000166114 likely benign Ataxia-telangiectasia syndrome 2021-12-16 criteria provided, single submitter clinical testing
GeneDx RCV000212026 SCV000167092 benign not specified 2014-01-24 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 RCV000123749 SCV000212916 likely benign Hereditary cancer-predisposing syndrome 2014-06-23 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Color Diagnostics, LLC DBA Color Health RCV000123749 SCV000537419 likely benign Hereditary cancer-predisposing syndrome 2015-07-21 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588006 SCV000694296 benign not provided 2017-07-21 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000588006 SCV000805575 likely benign not provided 2017-08-24 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000588006 SCV001249807 likely benign not provided 2021-12-01 criteria provided, single submitter clinical testing
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario RCV001798394 SCV002042257 likely benign Breast and/or ovarian cancer 2020-03-24 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000212026 SCV002065098 likely benign not specified 2018-02-26 criteria provided, single submitter clinical testing
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State RCV002225391 SCV002504724 likely benign Hereditary breast ovarian cancer syndrome 2022-04-19 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000123749 SCV002527767 likely benign Hereditary cancer-predisposing syndrome 2021-06-03 criteria provided, single submitter curation
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001358457 SCV001554197 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The ATM p.Asn1660 variant was identified in the literature however the frequency of this variant in an affected population was not provided. The variant was present in 1 of 562 control chromosomes (frequency: 0.002) from healthy individuals (Skowronska 2012). The variant was also identified in dbSNP (ID: rs144338238) as With Likely benign allele, ClinVar (classified as benign by GeneDx; classified as likely benign by Invitae, Ambry Genetics, Color Genomics), databases. The variant was not identified in GeneInsight-COGR, Cosmic, MutDB, LOVD 3.0, ATM-LOVD, databases. The variant was identified in control databases in 68 of 276658 chromosomes at a frequency of 0.000246 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The p.Asn1660= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000588006 SCV001809633 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute RCV000588006 SCV001905954 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000588006 SCV001931914 likely benign not provided no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000588006 SCV001959363 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000588006 SCV001975463 likely benign not provided no assertion criteria provided clinical testing

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