ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.1799_1802+5del

dbSNP: rs781244480
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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 RCV001379569 SCV001577393 likely pathogenic Ataxia-telangiectasia syndrome 2023-07-12 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant results in the deletion of part of exon 11 (c.1799_1802+5del) 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 present in population databases (rs781244480, gnomAD 0.0009%). 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: 1068117). 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 RCV002413907 SCV002716901 uncertain significance Hereditary cancer-predisposing syndrome 2022-08-16 criteria provided, single submitter clinical testing The c.1799_1802+5delACAGGTAAT variant results from a deletion of 9 nucleotides between positions c.1799 and c.1802+5 and involves the canonical splice donor site after coding exon 10 of the ATM gene. The canonical splice donor site is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site; however, direct evidence is insufficient at this time (Ambry internal data). The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNA decay; however, direct evidence is unavailable. The exact functional effect of the altered amino acid sequence is unknown. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
BRCAlab, Lund University RCV003155975 SCV002589103 likely pathogenic Familial cancer of breast 2022-08-26 no assertion criteria provided clinical testing

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