ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.5071A>C (p.Ser1691Arg) (rs1800059)

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Total submissions: 19
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000120143 SCV000149113 likely benign not specified 2017-11-22 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 RCV000119119 SCV000153832 benign Ataxia-telangiectasia syndrome 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000115204 SCV000187022 benign Hereditary cancer-predisposing syndrome 2014-06-23 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000120143 SCV000345515 benign not specified 2016-08-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000120143 SCV000602571 likely benign not specified 2017-03-27 criteria provided, single submitter clinical testing
Color RCV000115204 SCV000682248 likely benign Hereditary cancer-predisposing syndrome 2014-12-04 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000119119 SCV000743730 likely benign Ataxia-telangiectasia syndrome 2017-06-02 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000119119 SCV000745128 likely benign Ataxia-telangiectasia syndrome 2016-04-21 criteria provided, single submitter clinical testing
Counsyl RCV000119119 SCV000793059 likely benign Ataxia-telangiectasia syndrome 2017-07-26 criteria provided, single submitter clinical testing
SIB Swiss Institute of Bioinformatics RCV000119119 SCV000803488 benign Ataxia-telangiectasia syndrome 2018-05-31 criteria provided, single submitter curation This variant is interpreted as a Benign, for Ataxia-telangiectasia, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: BS2 => Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age. BP4 => Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.). BS3 => Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing (PMID:19431188).
PreventionGenetics,PreventionGenetics RCV000679127 SCV000805577 likely benign not provided 2016-12-12 criteria provided, single submitter clinical testing
Mendelics RCV000119119 SCV000838550 benign Ataxia-telangiectasia syndrome 2018-07-02 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000120143 SCV000916551 benign not specified 2017-09-19 criteria provided, single submitter clinical testing Variant summary: The ATM c.5071A>C (p.Ser1691Arg) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 493/276958 control chromosomes (3 homozygotes) at a frequency of 0.001780, which is approximately 2 times the estimated maximal expected allele frequency of a pathogenic ATM variant (0.0010005), suggesting this variant is likely a benign polymorphism. The variant has been reported in multiple breast cancer cases and cancer families, and in one ataxia-telangiectasia patient. None of the publications provide strong evidence for causality, lacking co-occurrence and co-segregation data, and often not providing the BRCA status of affected individuals. Multiple reputable clinical labs have classified this variant as likely benign/benign, without evidence to independently evaluate. Taken together, based on the prevalence in general population and by applying ACMG rules, the variant was classified as benign.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000679127 SCV001148431 likely benign not provided 2019-07-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000119119 SCV001260625 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.
ITMI RCV000120143 SCV000084283 not provided not specified 2013-09-19 no assertion provided reference population
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000119119 SCV000732993 likely benign Ataxia-telangiectasia syndrome no assertion criteria provided clinical testing
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam RCV000119119 SCV000745816 likely benign Ataxia-telangiectasia syndrome 2017-10-26 no assertion criteria provided clinical testing
True Health Diagnostics RCV000115204 SCV000787870 likely benign Hereditary cancer-predisposing syndrome 2017-11-14 no assertion criteria provided clinical testing

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