ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.2805G>C (p.Thr935=) (rs55934812)

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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000122836 SCV000166094 benign Ataxia-telangiectasia syndrome 2020-12-08 criteria provided, single submitter clinical testing
GeneDx RCV000211989 SCV000167075 benign not specified 2013-10-15 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 RCV000123732 SCV000212981 likely benign Hereditary cancer-predisposing syndrome 2014-08-19 criteria provided, single submitter clinical testing In silico models in agreement (benign);Synonymous alterations with insufficient evidence to classify as benign
Color Health, Inc RCV000123732 SCV000537452 likely benign Hereditary cancer-predisposing syndrome 2015-04-27 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000211989 SCV000694235 likely benign not specified 2020-10-22 criteria provided, single submitter clinical testing
Counsyl RCV000122836 SCV000792119 likely benign Ataxia-telangiectasia syndrome 2017-06-08 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000586912 SCV000805527 likely benign not provided 2017-04-03 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000586912 SCV001143102 benign not provided 2018-09-17 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000122836 SCV001263807 uncertain significance Ataxia-telangiectasia syndrome 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Natera, Inc. RCV000122836 SCV001461095 likely benign Ataxia-telangiectasia syndrome 2020-04-17 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001357062 SCV001552395 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The ATM p.Thr935= variant was identified in 4 of 5562 proband chromosomes (frequency: 0.001) from individuals or families with contralateral breast cancer, breast carcinoma or chronic lymphocytic leukemia (Bernstein 2010, Mangone 2015, Skowronska 2012, Teraoka 2001). The variant was also identified in dbSNP (ID: rs55934812) as "With Likely benign, Uncertain significance allele", ClinVar (classified as benign by GeneDx; as likely benign by Invitae, Ambry Genetics, Color Genomics; as uncertain significance by Integrated Genetics/Laboratory Corporation of America), and in LOVD 3.0 (1x as likely benign). The variant was not identified in COGR, and Cosmic databases. The variant was identified in control databases in 81 of 277128 chromosomes (1 homozygous) at a frequency of 0.0003 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 2 of 24032 chromosomes (freq: 0.0001), Other in 5 of 6464 chromosomes (freq: 0.001), Latino in 14 of 34420 chromosomes (freq: 0.0004), and European in 60 of 126690 chromosomes (freq: 0.001); it was not observed in the Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. The p.Thr935= 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 RCV000586912 SCV001809122 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000586912 SCV001919545 likely benign not provided no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000586912 SCV001956454 likely benign not provided no assertion criteria provided clinical testing

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