ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.8730C>G (p.Leu2910=) (rs551041839)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001084626 SCV000166149 benign Ataxia-telangiectasia syndrome 2020-11-25 criteria provided, single submitter clinical testing
Ambry Genetics RCV000164225 SCV000214846 likely benign Hereditary cancer-predisposing syndrome 2014-10-24 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.
GeneDx RCV000444064 SCV000512184 benign not specified 2015-08-14 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.
Color Health, Inc RCV000164225 SCV000682510 likely benign Hereditary cancer-predisposing syndrome 2015-07-27 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000444064 SCV000694384 likely benign not specified 2019-10-26 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000444064 SCV000805631 benign not specified 2017-05-15 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001356058 SCV001551118 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The ATM p.Leu2910= variant was not identified in the literature nor was it identified in the GeneInsight-COGR, Cosmic, MutDB, LOVD 3.0, or in ATM-LOVD databases. The variant was identified in dbSNP (ID: rs551041839) as "With Likely benign allele", ClinVar (classified as benign by Invitae, GeneDx; as likely benign by Ambry Genetics, Color Genomics, Integrated Genetics/Laboratory Corporation of America), and Clinvitae databases. The variant was identified in control databases in 153 of 246230 chromosomes (1 homozygous) at a frequency of 0.001 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include South Asian in 151 of 30782 chromosomes (freq: 0.004905), and Ashkenazi Jewish in 2 of 9848 chromosomes (freq: 0.0002) while the variant was not observed in the African, Other, Latino, European, East Asian, or Finnish populations. The p.Leu2910= 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 the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001573723 SCV001800012 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000444064 SCV001808788 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV001573723 SCV001953520 likely benign not provided no assertion criteria provided clinical testing

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