ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.7494T>C (p.Ser2498=) (rs34393781)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000212070 SCV000209576 benign not specified 2014-07-16 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 RCV000159594 SCV000213204 likely benign Hereditary cancer-predisposing syndrome 2014-07-16 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.
Invitae RCV000205045 SCV000260316 likely benign Ataxia-telangiectasia syndrome 2020-12-03 criteria provided, single submitter clinical testing
Color Health, Inc RCV000159594 SCV000537460 likely benign Hereditary cancer-predisposing syndrome 2015-07-24 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000212070 SCV000694354 likely benign not specified 2019-06-20 criteria provided, single submitter clinical testing
Counsyl RCV000205045 SCV000788910 likely benign Ataxia-telangiectasia syndrome 2016-12-23 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000589020 SCV000840961 uncertain significance not provided 2018-04-26 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000589020 SCV001246118 likely benign not provided 2019-12-01 criteria provided, single submitter clinical testing
Natera, Inc. RCV000205045 SCV001452135 likely benign Ataxia-telangiectasia syndrome 2020-04-18 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001356383 SCV001551535 likely benign Carcinoma of colon no assertion criteria provided clinical testing The ATM p.Ser2498= variant was not identified in the literature nor was it identified in the LOVD 3.0 database. The variant was identified in dbSNP (rs34393781) as “with uncertain significance allele”, ClinVar (interpreted as "likely benign" by Invitae and 3 others, "uncertain significance" by Integrated Genetics and "benign" by GeneDx). The variant was identified in control databases in 17 of 276,992 chromosomes at a frequency of 0.00006 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 2 of 24,032 chromosomes (freq: 0.00008), European in 15 of 126,500 chromosomes (freq: 0.0001), but not in the Other, Latino, Ashkenazi Jewish, East Asian, Finnish and South Asian populations. The p.Ser2498= 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. The nucleotide is not highly conserved among mammals and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) 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.

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