ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.1986T>C (p.Phe662=) (rs1800055)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000586136 SCV000166086 benign not provided 2019-03-04 criteria provided, single submitter clinical testing
GeneDx RCV000211971 SCV000167067 benign not specified 2014-01-17 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 RCV000123724 SCV000213136 likely benign Hereditary cancer-predisposing syndrome 2014-08-07 criteria provided, single submitter clinical testing
Color RCV000123724 SCV000537413 likely benign Hereditary cancer-predisposing syndrome 2015-08-14 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000586136 SCV000602570 likely benign not provided 2017-05-09 criteria provided, single submitter clinical testing The c.1986T>C variant (rs1800055) does not alter the amino acid sequence of the ATM protein and computational splice site prediction algorithms do not predict a change in the nearest splice site or creation of a cryptic splice site. This variant has not been reported in association with ataxia-telangiectasia or primary antibody deficiency in medical literature or in gene specific variation databases. This variant is listed in the NHLBI GO Exome Sequencing Project with an overall population frequency of 0.04 percent (identified on 5 out of 12,998 chromosomes) and is listed in the Exome Aggregation Consortium Browser with an overall population frequency of 0.042 percent (identified on 51 out of 121,356 chromosomes). Based on these observations, the c.1986T>C variant is likely to be benign.
Institute for Biomarker Research,Medical Diagnostic Laboratories, L.L.C. RCV000123724 SCV000679688 likely benign Hereditary cancer-predisposing syndrome 2017-07-12 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586136 SCV000694206 likely benign not provided 2016-05-10 criteria provided, single submitter clinical testing Variant summary: The c.1986TC (p.Phe662=) in ATM gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 0.00042 (51/121482 chrs tested), exclusively in individuals of European origin (0.0007; 48/66708 control chrs). This frequency exceeds the maximal expected frequency of a pathogenic allele (0.0005) in this gene. The variant of interest was cited as Likely Benign/Benign by reputable database/clinical laboratories. It is widely accepted as a rare polymorphism in the field. Taking together, the variant was classified as Likely Benign.
Counsyl RCV000122829 SCV000788483 likely benign Ataxia-telangiectasia syndrome 2018-03-29 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000123724 SCV000787848 likely benign Hereditary cancer-predisposing syndrome 2017-11-09 no assertion criteria provided clinical testing

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