ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.5410A>T (p.Ile1804Phe)

gnomAD frequency: 0.00001  dbSNP: rs769872474
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000205064 SCV000259341 uncertain significance Ataxia-telangiectasia syndrome 2024-01-21 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 1804 of the ATM protein (p.Ile1804Phe). This variant is present in population databases (rs769872474, gnomAD 0.004%). This missense change has been observed in individual(s) with breast cancer (PMID: 19781682, 28779002, 29596542, 34326862). ClinVar contains an entry for this variant (Variation ID: 219462). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV000570407 SCV000672627 likely benign Hereditary cancer-predisposing syndrome 2024-01-03 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
Counsyl RCV000205064 SCV000799847 uncertain significance Ataxia-telangiectasia syndrome 2018-05-11 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000570407 SCV000903393 uncertain significance Hereditary cancer-predisposing syndrome 2019-01-26 criteria provided, single submitter clinical testing
GeneDx RCV001785516 SCV002027917 uncertain significance not provided 2021-11-18 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 19781682, 28779002, 29596542, 16832357)
Sema4, Sema4 RCV000570407 SCV002528453 uncertain significance Hereditary cancer-predisposing syndrome 2021-07-20 criteria provided, single submitter curation
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. RCV000570407 SCV001977067 uncertain significance Hereditary cancer-predisposing syndrome 2021-09-27 no assertion criteria provided clinical testing
Natera, Inc. RCV000205064 SCV002081915 uncertain significance Ataxia-telangiectasia syndrome 2020-07-23 no assertion criteria provided clinical testing

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