Total submissions: 5
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Labcorp Genetics |
RCV001042076 | SCV001205738 | likely pathogenic | Ataxia-telangiectasia syndrome | 2023-07-06 | criteria provided, single submitter | clinical testing | 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 840154). Disruption of this splice site has been observed in individual(s) with clinical features of ataxia-telangiectasia (PMID: 21665257). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 25 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). |
| Ambry Genetics | RCV003283884 | SCV004007304 | likely pathogenic | Hereditary cancer-predisposing syndrome | 2023-05-16 | criteria provided, single submitter | clinical testing | The c.3746+1G>T intronic variant results from a G to T substitution one nucleotide after coding exon 24 of the ATM gene. This variant was reported in 1/60,466 breast cancer cases and in 0/53,461 controls (Dorling et al. N Engl J Med 2021 02;384:428-439). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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. 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. |
| Gene |
RCV003322843 | SCV004028092 | likely pathogenic | not provided | 2023-02-21 | criteria provided, single submitter | clinical testing | Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge |
| Myriad Genetics, |
RCV004031272 | SCV004932207 | likely pathogenic | Familial cancer of breast | 2024-01-22 | criteria provided, single submitter | clinical testing | This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. |
| Laboratory for Genotyping Development, |
RCV003160284 | SCV002758245 | pathogenic | Gastric cancer | 2021-07-01 | no assertion criteria provided | research |