ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.3078-5T>C

dbSNP: rs1565427457
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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 RCV001043104 SCV001206819 uncertain significance Ataxia-telangiectasia syndrome 2024-04-10 criteria provided, single submitter clinical testing This sequence change falls in intron 20 of the ATM gene. It does not directly change the encoded amino acid sequence of the ATM protein. This variant is not present in population databases (gnomAD no frequency). 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: 840977). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 RCV002319651 SCV002608647 likely pathogenic Hereditary cancer-predisposing syndrome 2023-09-01 criteria provided, single submitter clinical testing The c.3078-5T>C intronic variant results from a T to C substitution 5 nucleotides upstream from coding exon 20 in the ATM gene. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Another alteration impacting the same acceptor site (c.3078-1G>A) has been shown to have a similar impact on splicing and has been reported in the compound heterozygous state in an individual with ataxia-telangiectasia. Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Myriad Genetics, Inc. RCV004590044 SCV005085248 likely pathogenic Familial cancer of breast 2024-09-16 criteria provided, single submitter clinical testing This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad internal data].

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