ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.3118A>G (p.Met1040Val) (rs3092857)

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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000116423 SCV000167077 benign not specified 2013-11-26 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 RCV000123734 SCV000212921 benign Hereditary cancer-predisposing syndrome 2014-11-21 criteria provided, single submitter clinical testing
Invitae RCV000203947 SCV000262038 benign Ataxia-telangiectasia syndrome 2019-12-31 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224788 SCV000281553 likely benign not provided 2015-08-19 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
PreventionGenetics,PreventionGenetics RCV000116423 SCV000301659 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000203947 SCV000367040 benign Ataxia-telangiectasia syndrome 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Institute for Biomarker Research,Medical Diagnostic Laboratories, L.L.C. RCV000123734 SCV000576459 likely benign Hereditary cancer-predisposing syndrome 2017-02-14 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000203947 SCV000602561 benign Ataxia-telangiectasia syndrome 2019-02-27 criteria provided, single submitter clinical testing
Color RCV000123734 SCV000682103 benign Hereditary cancer-predisposing syndrome 2015-02-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000224788 SCV000694249 benign not provided 2016-06-06 criteria provided, single submitter clinical testing Variant summary: The ATM c.3118A>G (p.Met1040Val) variant involves the alteration of a non-conserved nucleotide. 3/3 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 459/122598 control chromosomes (10 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0413846 (428/10342, 10 homozygotes). This frequency is about 10 times the estimated maximal expected allele frequency of a pathogenic ATM variant (0.0039528), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. Variant has been reported by multiple studies in both patients and healthy controls, supporting the non-pathogenic nature of this variant. In addition, multiple clinical diagnostic laboratories classified this variant as benign. Considering the high allele frequency of the variant and the homozygous occurrences in the African subpopulation, it was classified as Benign.
OMIM RCV000003166 SCV000023324 pathogenic B-cell non-Hodgkin lymphoma 1997-09-01 no assertion criteria provided literature only
ITMI RCV000116423 SCV000084268 not provided not specified 2013-09-19 no assertion provided reference population
Genetic Services Laboratory,University of Chicago RCV000116423 SCV000150348 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
True Health Diagnostics RCV000123734 SCV000787858 likely benign Hereditary cancer-predisposing syndrome 2018-01-05 no assertion criteria provided clinical testing

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