ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.6199-3T>C

gnomAD frequency: 0.00003  dbSNP: rs1318760213
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000567488 SCV000665582 uncertain significance Hereditary cancer-predisposing syndrome 2021-03-24 criteria provided, single submitter clinical testing The c.6199-3T>C intronic variant results from a T to C substitution 3 nucleotides upstream from coding exon 42 in the ATM gene. This nucleotide position is poorly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV001370807 SCV001567344 uncertain significance Ataxia-telangiectasia syndrome 2022-02-21 criteria provided, single submitter clinical testing 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. 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. ClinVar contains an entry for this variant (Variation ID: 481282). This variant has not been reported in the literature in individuals affected with ATM-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change falls in intron 42 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.
Myriad Genetics, Inc. RCV004592682 SCV005083815 likely benign Familial cancer of breast 2024-06-05 criteria provided, single submitter clinical testing This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing.

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