ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.5248G>T (p.Ala1750Ser)

gnomAD frequency: 0.00035  dbSNP: rs771897046
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV000989489 SCV001139902 likely benign Fanconi anemia complementation group A 2019-05-28 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV002256643 SCV002529378 likely benign Fanconi anemia 2022-02-28 criteria provided, single submitter curation
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001358243 SCV001553919 uncertain significance not provided no assertion criteria provided clinical testing The SLX4 p.A1750S variant was not identified in the literature but was identified in dbSNP (ID: rs771897046) and ClinVar (classified as likely benign by Mendelics). The variant was identified in control databases in 51 of 281696 chromosomes at a frequency of 0.0001810, and was observed at the highest frequency in the East Asian population in 50 of 19912 chromosomes (freq: 0.002511) (Genome Aggregation Database March 6, 2019, v2.1.1). The p.A1750 residue is conserved in mammals but not in more distantly related organisms and computational analyses (MUT Assesor, PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (Splice AI exome) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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