ClinVar Miner

Submissions for variant NM_003331.5(TYK2):c.648G>A (p.Pro216=) (rs142642403)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
AIC-CCMB Diagnostics Facility, CSIR - Centre for Cellular and Molecular Biology RCV000984870 SCV001073395 uncertain significance Immunodeficiency; Recurrent skin infections 2019-10-10 criteria provided, single submitter clinical testing The c.648G>A variant is present in publicly available databases like 1000 Genomes, EVS, ExAC, gnomAD and dbSNP at very low minor allele frequency (<0.0002), in heterozygous state. The variant is also not present in our in-house exome database. This variant was also not reported earlier in OMIM, ClinVar and HGMD databases in any other affected individuals. In-silico splice-site aberration prediction program Human Splice Finder version 3.1 (HSF) predicted possible effect of splicing due to alteration of an exonic splicing enhancer (ESE) region by this variant. In-silico pathogenicity prediction programs like Mutation Taster2 and CADD predicted this variant as likely deleterious. However there are no functional studies performed earlier. Due to lack of enough evidence and also considering the phenotype of the patient the variant has been classified as uncertain significance as per the ACMG guidelines. The variant was observed in this patient with an another heterozygous variant (c.1694G>A) in TYK2 gene.
Invitae RCV000970668 SCV001118261 likely benign Immunodeficiency 35 2020-12-06 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000970668 SCV001284810 uncertain significance Immunodeficiency 35 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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