ClinVar Miner

Submissions for variant NM_020458.4(TTC7A):c.2018-1G>C

gnomAD frequency: 0.00002  dbSNP: rs948534045
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001776614 SCV002013295 likely pathogenic not provided 2021-05-26 criteria provided, single submitter clinical testing Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Identified in the heterozygous state and described as c.2090-1G>C due to alternate nomenclature, in a patient with gastrointestinal defects and immunodeficiency syndrome (Hou et al., 2020); This variant is associated with the following publications: (PMID: 31980526)
Revvity Omics, Revvity RCV003147653 SCV002022461 pathogenic Gastrointestinal defects and immunodeficiency syndrome 1 2019-08-22 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001780445 SCV002291699 likely pathogenic Multiple gastrointestinal atresias 2024-07-12 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 17 of the TTC7A 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 TTC7A are known to be pathogenic (PMID: 23830146, 24292712). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with TTC7A-related conditions. ClinVar contains an entry for this variant (Variation ID: 1320635). 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.
AiLife Diagnostics, AiLife Diagnostics RCV001776614 SCV002502684 likely pathogenic not provided 2022-03-30 criteria provided, single submitter clinical testing

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