ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.7089+3A>G

dbSNP: rs1565524203
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000703114 SCV000831996 uncertain significance Ataxia-telangiectasia syndrome 2022-07-25 criteria provided, single submitter clinical testing This sequence change falls in intron 48 of the ATM gene. It does not directly change the encoded amino acid sequence of the ATM protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast cancer (PMID: 31465090). ClinVar contains an entry for this variant (Variation ID: 579751). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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.
Color Diagnostics, LLC DBA Color Health RCV001183564 SCV001349354 uncertain significance Hereditary cancer-predisposing syndrome 2018-12-05 criteria provided, single submitter clinical testing
Ambry Genetics RCV001183564 SCV002662560 uncertain significance Hereditary cancer-predisposing syndrome 2024-04-16 criteria provided, single submitter clinical testing The c.7089+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 47 in the ATM gene. This variant was identified in a cohort of individuals diagnosed with metastatic breast cancer who underwent germline testing of 30 genes (Stuttgen K et al. JAMA Oncol, 2019 Oct;5:1506-1508). This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Based on the available evidence, the clinical significance of this variant remains unclear.

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