ClinVar Miner

Submissions for variant NM_006642.5(SDCCAG8):c.220+2T>C

gnomAD frequency: 0.00003  dbSNP: rs757796329
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000778231 SCV000914399 uncertain significance SDCCAG8-related disorder 2018-11-23 criteria provided, single submitter clinical testing The SDCCAG8 c.220+2T>C variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. A literature search was performed for the gene and cDNA change. No publications were found based on this search. The c.220+2T>C variant is reported at a frequency of 0.000853 in the East Asian population from the Genome Aggregation Database. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of splice donor variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for SDCCAG8-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Labcorp Genetics (formerly Invitae), Labcorp RCV001378522 SCV001576106 likely pathogenic Senior-Loken syndrome 7; Bardet-Biedl syndrome 16 2022-09-27 criteria provided, single submitter clinical testing This variant is present in population databases (rs757796329, gnomAD 0.08%). 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: 631600). This variant has not been reported in the literature in individuals affected with SDCCAG8-related conditions. This sequence change affects a donor splice site in intron 2 of the SDCCAG8 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 SDCCAG8 are known to be pathogenic (PMID: 20835237, 22190896).

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