ClinVar Miner

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

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000115235 SCV000183909 benign Hereditary cancer-predisposing syndrome 2014-07-12 criteria provided, single submitter clinical testing
Color RCV000115235 SCV000682374 likely benign Hereditary cancer-predisposing syndrome 2014-12-08 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
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.
Genetic Services Laboratory, University of Chicago RCV000120155 SCV000593490 likely benign not specified 2017-03-06 criteria provided, single submitter clinical testing
ITMI RCV000120155 SCV000084296 not provided not specified 2013-09-19 no assertion provided reference population
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.
Invitae RCV000119129 SCV000153843 benign Ataxia-telangiectasia syndrome 2018-01-07 criteria provided, single submitter clinical testing
PreventionGenetics RCV000120155 SCV000805609 benign not specified 2017-05-26 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000115235 SCV000787878 likely benign Hereditary cancer-predisposing syndrome 2017-08-11 no assertion criteria provided clinical testing

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