ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.4167A>G (p.Thr1389=) (rs183214437)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000212010 SCV000167088 benign not specified 2014-03-13 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 RCV000123745 SCV000212975 benign Hereditary cancer-predisposing syndrome 2014-10-10 criteria provided, single submitter clinical testing This alteration is classified as 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 RCV000988683 SCV000282955 likely benign Ataxia-telangiectasia syndrome 2020-11-23 criteria provided, single submitter clinical testing
Color Health, Inc RCV000123745 SCV000537429 likely benign Hereditary cancer-predisposing syndrome 2016-07-18 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000212010 SCV000694274 likely benign not specified 2019-08-20 criteria provided, single submitter clinical testing
Mendelics RCV000988683 SCV001138500 likely benign Ataxia-telangiectasia syndrome 2019-05-28 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000212010 SCV001549118 benign not specified no assertion criteria provided clinical testing The ATM p.Thr1389= variant was not identified in the literature nor was it identified in the Genesight-COGR, Cosmic, MutDB, LOVD 3.0, ATM-LOVD, databases. The variant was identified in dbSNP (ID: rs183214437) as “with other allele”, in ClinVar and Clinvitae databases as benign by GeneDx and Ambry Genetics; and likely benign by Invitae, and Color Genomics Inc.). The variant was identified in control databases in 29 of 277012 chromosomes at a frequency of 0.0001 in the following populations: African in 1 of 24024 chromosomes (freq. 0.00004), Latino in 7 of 34400 chromosomes (freq. 0.0002), European Non-Finnish in 18 of 126560 chromosomes (freq. 0.0001), Other in 3of 6458 chromosomes (freq. 0.0005), but was not seen in Ashkenazi Jewish, East Asian , European Finnish, and South Asian populations, increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The p.Thr1389= 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 this variant meets our laboratory's criteria to be classified as benign.

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