ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.162T>C (p.Tyr54=) (rs3218690)

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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000119217 SCV000153959 benign Ataxia-telangiectasia syndrome 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000211941 SCV000167080 benign not specified 2013-10-23 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 RCV000123737 SCV000213023 likely benign Hereditary cancer-predisposing syndrome 2014-06-20 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000415913 SCV000493479 likely benign not provided 2020-02-01 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000211941 SCV000593474 likely benign not specified 2017-03-15 criteria provided, single submitter clinical testing
Color RCV000123737 SCV000681988 benign Hereditary cancer-predisposing syndrome 2015-04-25 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000415913 SCV000694189 benign not provided 2016-01-11 criteria provided, single submitter clinical testing Variant summary: This c.162T>C variant affects a non-conserved nucleotide, resulting in synonymous amino acid change. 5/5 splice-site tools via Alamut predict that this variant does not affect normal splicing. This variant was found in 208/121226 control chromosomes (including the large and broad populations of ExAC) at a frequency of 0.0017158, which does not exceed the maximal expected frequency of a pathogenic allele (0.0039528) in this gene. However, the possibility that this variant can still represents as a rare polymorphism cannot be ruled out from the comparison. The variant is more common in European (Non-Finnish) population where its allele frequency is 0.25% (167/66625 chromosomes) including one homozygous occurrence. The homozygote is suggestive of a benign outcome with respect to early onset recessive phenotype A-T. [Penetrance of variants causing A-T is not exactly known.] This variant has been found in patients with A-T, breast and/or ovarian cancer, chronic lymphocytic leukemia and Hodgkins lymphoma. The publications reporting patient occurrences report this variant as polymorphism. In one A-T patient reported, the patient also carried other two potentially pathogenic variants (Buzin_2003), suggesting a benign outcome for this variant. In addition, this variant was found at similar frequencies in a small case-control study (Liberzon_2004), further supporting a benign outcome. Multiple clinical labs have classified this variant as benign/likely benign. Taken together, this variant has been classified as Benign.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000211941 SCV000704532 likely benign not specified 2016-12-20 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000119217 SCV000745120 likely benign Ataxia-telangiectasia syndrome 2017-06-28 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000211941 SCV000805500 benign not specified 2017-08-25 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000415913 SCV000840919 benign not provided 2018-08-21 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000415913 SCV000885034 likely benign not provided 2017-12-26 criteria provided, single submitter clinical testing The c.162T>C variant (rs3218690) 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 in medical literature or in gene specific variation databases. This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.18 percent (identified on 486 out of 276,848 chromosomes) and has been reported to ClinVar (Variation ID: 132757). Based on these observations, the c.162T>C variant is likely to be benign.
Illumina Clinical Services Laboratory,Illumina RCV000119217 SCV001265965 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.
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam RCV000119217 SCV000745801 benign Ataxia-telangiectasia syndrome 2017-09-27 no assertion criteria provided clinical testing
True Health Diagnostics RCV000123737 SCV000787846 likely benign Hereditary cancer-predisposing syndrome 2018-01-03 no assertion criteria provided clinical testing

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