ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.5793T>C (p.Ala1931=) (rs3092910)

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Total submissions: 19
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000119174 SCV000153905 benign Ataxia-telangiectasia syndrome 2020-12-07 criteria provided, single submitter clinical testing
GeneDx RCV000116428 SCV000167095 benign not specified 2013-10-10 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 RCV000123752 SCV000212674 likely benign Hereditary cancer-predisposing syndrome 2015-09-04 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics,PreventionGenetics RCV000116428 SCV000301676 likely benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000116428 SCV000334466 benign not specified 2015-09-08 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000416115 SCV000493543 likely benign not provided 2016-07-01 criteria provided, single submitter clinical testing
Color Health, Inc RCV000123752 SCV000537381 benign Hereditary cancer-predisposing syndrome 2015-04-10 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000116428 SCV000538368 likely benign not specified 2016-03-28 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Silent variant not near splice site
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001282737 SCV000602553 benign none provided 2020-08-18 criteria provided, single submitter clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000119174 SCV000745129 likely benign Ataxia-telangiectasia syndrome 2017-06-28 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000119174 SCV001262765 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.
Athena Diagnostics Inc RCV000116428 SCV001879509 benign not specified 2020-11-25 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000116428 SCV000150353 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 RCV000123752 SCV000787874 likely benign Hereditary cancer-predisposing syndrome 2018-02-20 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001355317 SCV001550175 benign Malignant tumor of breast no assertion criteria provided clinical testing The ATM p.Ala1931= variant was identified in 3 of 572 proband chromosomes (frequency: 0.005) from North American caucasian and American Indian individuals or families with Non-Hodgkin’s Lymphoma, or undisclosed cancer; and was present in 1 of 186 control chromosomes (frequency: 0.005) from healthy individuals (Sipahimalani 2007, Petereit 2013, Thorstenson 2001). Thorstenson et al (2001) showed that ATM shows overall low sequence diversity, when compared across 7 major human populations. The variant was also identified in dbSNP (ID: rs3092910) “With other allele”, ClinVar (classified as benign by Invitae, GeneDx, EGL Genetic Diagnostics (Eurofins Clinical Diagnostics), Color Genomics Inc; and likely benign by Ambry Genetics, Prevention Genetics, Praxis fuer Humangenetik Tuebingen, Lab. for Molecular Medicine Partners HealthCare Personalized Medicine, and Genetic Services Laboratory (U of Chicago)), Clinvitae (5x), and was not identified in Genesight-COGR, Cosmic, MutDB, LOVD 3.0, and ATM-LOVD. The variant was identified in control databases in 1400 (6 homozygous) of 276860 chromosomes at a frequency of 0.005 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017), being identified in the following populations: African in 191 (1 homozygous) of 24012 chromosomes (frequency: 008), Other in 27 of 6450 chromosomes (frequency: 004), Latino in 45 of 34376 chromosomes (frequency: 001), European Non-Finnish in 828 (3 homozygous) of 126508 chromosomes (frequency: 007), Ashkenazi Jewish in 31 of 10146 chromosomes (frequency: 003), East Asian in 213 (2 homozygous) of 18848 chromosomes (frequency: 01), European Finnish in 20 of 25750 chromosomes (frequency: 0008), and South Asian in 45 of 30770 chromosomes (frequency: 001). The p.Ala1931= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000116428 SCV001808574 benign not specified no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute RCV000416115 SCV001906141 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000416115 SCV001917374 likely benign not provided no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000416115 SCV001953751 likely benign not provided no assertion criteria provided clinical testing

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