ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.6919C>T (p.Leu2307Phe) (rs56009889)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000120155 SCV000149144 benign not specified 2015-11-11 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 RCV000988720 SCV000153843 benign Ataxia-telangiectasia syndrome 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000115235 SCV000183909 benign Hereditary cancer-predisposing syndrome 2014-07-12 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000586678 SCV000342311 uncertain significance not provided 2016-05-20 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000120155 SCV000593490 benign not specified 2019-07-10 criteria provided, single submitter clinical testing
Color RCV000115235 SCV000682374 likely benign Hereditary cancer-predisposing syndrome 2014-12-08 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586678 SCV000694338 benign not provided 2017-01-03 criteria provided, single submitter clinical testing Variant summary: This c.6919C>T variant affects a conserved nucleotide, resulting in conservative amino acid change from Leu to Phe. 3/5 in-silico tools predict this variant to be damaging. This variant has been reported in patients with breast cancer, ovarian cancer, melanoma, lung cancer, CLL or Hodgkin's disease; however, without evidence on co-segregation analysis. In one family with familial CLL, this variant was found in one affected brother but not in the other affected brother (Yuille_2002) (ACMG, BS4). Additionally, in a patient with a history of Lynch syndrome, the variant co-occurred with a pathogenic MSH2 variant (Yurgelun_2015) (ACMG, BP5). This variant has not been reported in patients with Ataxia-Telangiectasia (a recessive disorder). This variant was found in 140/128300 control chromosomes including one homozygote (ACMG, BS2) from multiple ethnic populations at a frequency of 0.0010912, which is about 2 times greater than the maximal expected frequency of a pathogenic allele (0.0005001) in this gene, suggesting this variant is benign (ACMG, BS1). Multiple case-control studies have shown that this variant was not associated with breast cancer, except one study (Haiman_2013, OR=4.133 in mixed ethnic populations, OR=9.805 in European American). The study (Haiman_2013), however, did not provide confidence interval and distribution of the variant is patient and control cohorts appear to be small, not suggesting a believable odds ratio. Multiple clinical laboratories classified this variant as likely benign/benign (ACMG BP6). Taken together, this variant was classified as a Benign variant.
PreventionGenetics,PreventionGenetics RCV000120155 SCV000805609 benign not specified 2017-05-26 criteria provided, single submitter clinical testing
Mendelics RCV000988720 SCV001138554 likely benign Ataxia-telangiectasia syndrome 2019-05-28 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000988720 SCV001260752 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 RCV000120155 SCV000084296 not provided not specified 2013-09-19 no assertion provided reference population
True Health Diagnostics RCV000115235 SCV000787878 likely benign Hereditary cancer-predisposing syndrome 2017-08-11 no assertion criteria provided clinical testing

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