ClinVar Miner

Submissions for variant NM_003331.5(TYK2):c.44T>C (p.Val15Ala) (rs144960992)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV001082832 SCV000410315 likely benign Immunodeficiency 35 2018-01-12 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV000482893 SCV000573526 uncertain significance not provided 2017-02-20 criteria provided, single submitter clinical testing The V15A variant has not been published in association with Hyper-IgE syndrome or other related Mendelian disorders to our knowledge. It was observed in two heterozygous individuals with acute lymphoblastic leukemia (Kalender et al., 2012; Sanda et al., 2013). The variant is observed in 59/16464 (0.36%) alleles from individuals of South Asian background in the ExAC dataset, including 2 homozygous individuals (Lek et al., 2016). V15A is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is not conserved, and in silico analysis predicts this variant likely does not alter the protein structure/function. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV001082832 SCV000766978 benign Immunodeficiency 35 2020-11-16 criteria provided, single submitter clinical testing

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