ClinVar Miner

Submissions for variant NM_000080.4(CHRNE):c.1220-1G>C

dbSNP: rs373710822
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001065700 SCV001230672 likely pathogenic Congenital myasthenic syndrome 4A 2024-01-15 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 10 of the CHRNE 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 CHRNE are known to be pathogenic (PMID: 22678886). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CHRNE-related conditions. ClinVar contains an entry for this variant (Variation ID: 859561). 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.
CeGaT Center for Human Genetics Tuebingen RCV001093140 SCV001249977 pathogenic not provided 2020-01-01 criteria provided, single submitter clinical testing
GeneDx RCV001093140 SCV001789236 likely pathogenic not provided 2019-08-24 criteria provided, single submitter clinical testing Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge
Baylor Genetics RCV001065700 SCV004214235 likely pathogenic Congenital myasthenic syndrome 4A 2023-08-02 criteria provided, single submitter clinical testing
Natera, Inc. RCV001836104 SCV002093380 likely pathogenic Congenital myasthenic syndrome 2021-08-13 no assertion criteria provided clinical testing

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