ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.8592C>T (p.Tyr2864=) (rs56025670)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000988737 SCV000166146 benign Ataxia-telangiectasia syndrome 2020-12-02 criteria provided, single submitter clinical testing
GeneDx RCV000212088 SCV000167059 benign not specified 2014-02-10 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 RCV000123716 SCV000212941 likely benign Hereditary cancer-predisposing syndrome 2014-07-14 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 Health, Inc RCV000123716 SCV000537453 likely benign Hereditary cancer-predisposing syndrome 2015-06-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000212088 SCV000694381 likely benign not specified 2020-08-21 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000587103 SCV000805629 likely benign not provided 2017-09-15 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000587103 SCV000840966 likely benign not provided 2019-07-12 criteria provided, single submitter clinical testing
Mendelics RCV000988737 SCV001138583 likely benign Ataxia-telangiectasia syndrome 2019-05-28 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000587103 SCV001148453 likely benign not provided 2020-12-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001356318 SCV001551452 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The ATM p.Tyr2864= variant was identified in 6 of 5506 proband chromosomes (frequency: 0.001) from individuals or families with CLL, breast, or ovarian cancer (Bernstein 2010, Petereit 2013, Skowronska 2012, Thorstenson 2003). The variant was also identified in dbSNP (ID: rs56025670) as "With Likely benign allele ", ClinVar (classified as benign by GeneDx; as likely benign by Invitae, Ambry Genetics, Color Genomics, and Integrated Genetics/Laboratory Corporation of America), and in LOVD 3.0 (1x as likely benign). The variant was not identified in COGR, or Cosmic databases. The variant was identified in control databases in 124 of 275644 chromosomes at a frequency of 0.0005 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 5 of 23944 chromosomes (freq: 0.0002), Other in 1 of 6422 chromosomes (freq: 0.0002), Latino in 5 of 34318 chromosomes (freq: 0.0002), European in 113 of 125504 chromosomes (freq: 0.0009), while the variant was not observed in the Ashkenazi Jewish, East Asian, European Finnish, or South Asian populations. The p.Tyr2864= 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) 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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