ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.1163+5G>A

gnomAD frequency: 0.00001  dbSNP: rs762454252
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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 RCV001115354 SCV001273325 uncertain significance Fanconi anemia complementation group P 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.
Invitae RCV003635940 SCV004450066 uncertain significance Fanconi anemia 2023-04-04 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with SLX4-related conditions. 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. 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 may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 884337). This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 5 of the SLX4 gene. It does not directly change the encoded amino acid sequence of the SLX4 protein. It affects a nucleotide within the consensus splice site.

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