ClinVar Miner

Submissions for variant NM_001041.4(SI):c.5109-3T>C

gnomAD frequency: 0.00002  dbSNP: rs202110241
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001150113 SCV001311126 uncertain significance Sucrase-isomaltase deficiency 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV001882461 SCV002314680 uncertain significance not provided 2022-08-31 criteria provided, single submitter clinical testing This sequence change falls in intron 44 of the SI gene. It does not directly change the encoded amino acid sequence of the SI protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs202110241, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with SI-related conditions. ClinVar contains an entry for this variant (Variation ID: 903059). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Revvity Omics, Revvity RCV001150113 SCV003823205 uncertain significance Sucrase-isomaltase deficiency 2020-02-28 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV001882461 SCV005189864 uncertain significance not provided criteria provided, single submitter not provided

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