ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.6067G>A (p.Gly2023Arg) (rs11212587)

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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000120151 SCV000149130 likely benign not specified 2017-11-17 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.
Invitae RCV000122864 SCV000166122 benign Ataxia-telangiectasia syndrome 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000115221 SCV000183877 likely benign Hereditary cancer-predisposing syndrome 2018-07-27 criteria provided, single submitter clinical testing Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;Subpopulation frequency in support of benign classification
PreventionGenetics,PreventionGenetics RCV000120151 SCV000301678 benign not specified criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000513642 SCV000608617 likely benign not provided 2018-10-01 criteria provided, single submitter clinical testing
Color RCV000115221 SCV000687670 likely benign Hereditary cancer-predisposing syndrome 2015-02-11 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000513642 SCV000694314 benign not provided 2017-08-21 criteria provided, single submitter clinical testing Variant summary: The ATM c.6067G>A (p.Gly2023Arg) variant involves the alteration of a conserved nucleotide and 4/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 397/277154 (1 homozygote) control chromosomes (gnomAD), predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.002368 (300/126680). This frequency is about 2 times the estimated maximal expected allele frequency of a pathogenic ATM variant (0.0010005), suggesting this is likely a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. Multiple publications have cited the variant in affected BrC pts, along with multiple somatic occurrences in MCL and CLL pts. Skowronska_2012 suggestions, biallelic ATM inactivation in CLL patients was associated with disease progression and reduced survival. However, the variant has been reported to co-occur with a BRCA1 variant, although the exact variant was not indicated (Thorstenson_2003). In addition, two internal LCA samples report the variant to co-occur with a pathogenic ATM variant, c.6095G>A (p.Arg20232Lys) and BRCA1 variant, c.1326T>A (p.Cys442X). In addition, multiple clinical diagnostic laboratories cite the variant as "likely benign/benign." Taken together, this variant is classified as benign.
GeneKor MSA RCV000115221 SCV000821865 uncertain significance Hereditary cancer-predisposing syndrome 2018-08-01 criteria provided, single submitter clinical testing
Mendelics RCV000122864 SCV000838565 uncertain significance Ataxia-telangiectasia syndrome 2018-07-02 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000513642 SCV000840948 likely benign not provided 2018-06-13 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000122864 SCV001263992 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.
Institute of Human Genetics, University of Leipzig Medical Center RCV001253480 SCV001429203 uncertain significance Familial cancer of breast 2018-12-05 criteria provided, single submitter clinical testing
ITMI RCV000120151 SCV000084292 not provided not specified 2013-09-19 no assertion provided reference population
True Health Diagnostics RCV000115221 SCV000805219 uncertain significance Hereditary cancer-predisposing syndrome 2018-03-16 no assertion criteria provided clinical testing

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