ClinVar Miner

Submissions for variant NM_001025356.3(ANO6):c.1880+1G>A

gnomAD frequency: 0.00002  dbSNP: rs371269172
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Revvity Omics, Revvity RCV001783638 SCV002024339 pathogenic SCOTT SYNDROME 2019-10-30 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002544250 SCV003260413 likely pathogenic not provided 2022-07-11 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 15 of the ANO6 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 ANO6 are known to be pathogenic (PMID: 21107324, 21511967, 27879994). This variant is present in population databases (rs371269172, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ANO6-related conditions. ClinVar contains an entry for this variant (Variation ID: 1323274). 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.
PreventionGenetics, part of Exact Sciences RCV003401711 SCV004120391 uncertain significance ANO6-related disorder 2023-04-03 criteria provided, single submitter clinical testing The ANO6 c.1880+1G>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.013% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/12-45797320-G-A). Upstream variants that disrupt consensus splice sites in ANO6 have been reported as pathogenic. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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