ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.1229T>C (p.Val410Ala) (rs56128736)

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Total submissions: 18
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000120171 SCV000149045 benign not specified 2016-11-29 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.
Invitae RCV000119195 SCV000153936 benign Ataxia-telangiectasia syndrome 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000115136 SCV000172873 benign Hereditary cancer-predisposing syndrome 2014-07-13 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000120171 SCV000232902 likely benign not specified 2015-04-01 criteria provided, single submitter clinical testing
Vantari Genetics RCV000115136 SCV000266989 uncertain significance Hereditary cancer-predisposing syndrome 2016-01-22 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000120171 SCV000593497 uncertain significance not specified 2017-02-21 criteria provided, single submitter clinical testing
Color RCV000115136 SCV000681959 benign Hereditary cancer-predisposing syndrome 2015-11-05 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590142 SCV000694174 likely benign not provided 2016-06-10 criteria provided, single submitter clinical testing Variant summary: The ATM c.1229T>C (p.Val410Ala) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome (SNPs&GO not captured due to low reliability index). This variant was found in 270/126714 control chromosomes (2 homozygotes) at a frequency of 0.0021308, which is approximately 4 times the estimated maximal expected allele frequency of a pathogenic ATM variant (0.0005001), suggesting this variant is likely a benign polymorphism. This variant has been found in patients with various types of cancer, including breast cancer, uterine serous carcinoma, lymphoma, chronic lymphocytic leukemia, and melanoma. It has not been reported in patients with ataxia-telangiectasia. Two large case-control studies showed that this variant is not associated with breast cancer (Tavtigian 2009; Haiman 2013). Thus available patient and control data show that this variant is a polymorphism found in patients as well as unaffected individuals. In addition, three clinical laboratories have classified this variant as benign/likely benign albeit another lab consider it as uncertain significance, all without evidence to independently evaluate. Taken together, this variant has been classified as Likely benign until more evidence becomes available.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000590142 SCV000780400 uncertain significance not provided 2019-05-01 criteria provided, single submitter clinical testing
Counsyl RCV000119195 SCV000788575 likely benign Ataxia-telangiectasia syndrome 2017-05-18 criteria provided, single submitter clinical testing
Institute for Biomarker Research,Medical Diagnostic Laboratories, L.L.C. RCV000115136 SCV000803142 likely benign Hereditary cancer-predisposing syndrome 2018-05-23 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000590142 SCV000805492 likely benign not provided 2015-06-18 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000590142 SCV000840914 benign not provided 2017-09-11 criteria provided, single submitter clinical testing
Mendelics RCV000119195 SCV001138445 likely benign Ataxia-telangiectasia syndrome 2019-05-28 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000119195 SCV001157044 benign Ataxia-telangiectasia syndrome 2019-02-28 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000119195 SCV001263700 likely benign 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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
ITMI RCV000120171 SCV000084313 not provided not specified 2013-09-19 no assertion provided reference population
True Health Diagnostics RCV000115136 SCV000787842 likely benign Hereditary cancer-predisposing syndrome 2017-11-14 no assertion criteria provided clinical testing

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