ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.4909+4C>T

gnomAD frequency: 0.00001  dbSNP: rs587782125
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000130663 SCV000185549 uncertain significance Hereditary cancer-predisposing syndrome 2023-12-19 criteria provided, single submitter clinical testing The c.4909+4C>T intronic variant results from a C to T substitution 4 nucleotides after coding exon 31 in the ATM gene. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive and 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000460771 SCV000546908 pathogenic Ataxia-telangiectasia syndrome 2024-01-09 criteria provided, single submitter clinical testing This sequence change falls in intron 32 of the ATM gene. It does not directly change the encoded amino acid sequence of the ATM protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs587782125, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ATM-related conditions. ClinVar contains an entry for this variant (Variation ID: 141940). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in activation of a cryptic splice site and introduces a premature termination codon (Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
Color Diagnostics, LLC DBA Color Health RCV000130663 SCV000682227 uncertain significance Hereditary cancer-predisposing syndrome 2018-08-29 criteria provided, single submitter clinical testing
Counsyl RCV000460771 SCV000793093 uncertain significance Ataxia-telangiectasia syndrome 2017-08-01 criteria provided, single submitter clinical testing
Baylor Genetics RCV003467151 SCV004212161 uncertain significance Familial cancer of breast 2022-11-26 criteria provided, single submitter clinical testing
Natera, Inc. RCV000460771 SCV001462150 uncertain significance Ataxia-telangiectasia syndrome 2020-04-17 no assertion criteria provided clinical testing

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