ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.1898+3A>G

gnomAD frequency: 0.00001  dbSNP: rs200169643
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000542135 SCV000622292 benign Ataxia-telangiectasia syndrome 2024-01-16 criteria provided, single submitter clinical testing
Ambry Genetics RCV000571939 SCV000665580 uncertain significance Hereditary cancer-predisposing syndrome 2023-06-30 criteria provided, single submitter clinical testing The c.1898+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 11 in the ATM gene. This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing; however, direct evidence is insufficient at this time (Ambry internal data). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Color Diagnostics, LLC DBA Color Health RCV000571939 SCV000682013 uncertain significance Hereditary cancer-predisposing syndrome 2020-04-30 criteria provided, single submitter clinical testing This variant causes an A to G nucleotide substitution at the +3 position of intron 12 of the ATM gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. However, this prediction has not been confirmed in published RNA studies. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 5/281032 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario RCV003150259 SCV003837605 uncertain significance Breast and/or ovarian cancer 2021-10-14 criteria provided, single submitter clinical testing
GeneDx RCV003324759 SCV004031022 uncertain significance not provided 2023-08-26 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this variant does not alter splicing; Published RNA studies demonstrate no impact on splicing (Bueno-Martnez et al., 2022); Observed in an individual with pancreatic cancer (Terashima et al., 2022); This variant is associated with the following publications: (PMID: 36135357, 35716007)
Natera, Inc. RCV000542135 SCV002081628 uncertain significance Ataxia-telangiectasia syndrome 2021-05-19 no assertion criteria provided clinical testing

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