ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.3402+1G>A

dbSNP: rs1565439606
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001052757 SCV001216982 likely pathogenic Ataxia-telangiectasia syndrome 2023-11-20 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 23 of the ATM gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with ataxia-telangiectasia (PMID: 21665257). ClinVar contains an entry for this variant (Variation ID: 848905). 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 currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Ambry Genetics RCV002451217 SCV002612706 likely pathogenic Hereditary cancer-predisposing syndrome 2019-11-18 criteria provided, single submitter clinical testing The c.3402+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 22 of the ATM gene. This alteration, referred to as IVS25+1G>A by the authors, was reported as homozygous in an individual with ataxia-telangiectasia (Micol R et al. J Allergy Clin Immunol, 2011 Aug;128:382-9.e1). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.

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