ClinVar Miner

Submissions for variant NM_000215.3(JAK3):c.1442-5C>T (rs3212750)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000125432 SCV000168884 benign not specified 2014-04-29 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000544769 SCV000638314 benign Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-negative 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000125432 SCV000917545 benign not specified 2017-11-22 criteria provided, single submitter clinical testing Variant summary: The JAK3 c.1442-5C>T variant involves the alteration of a non-conserved nucleotide. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 582/277228 control chromosomes (6 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.022258 (535/24036 with 5 homozygotes). This frequency is about 21 times the estimated maximal expected allele frequency of a pathogenic JAK3 variant (0.0010801), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. This variant, to our knowledge, has not been reported via publications in affected individuals. In addition, one clinical diagnostic laboratory classified this variant as benign. Taken together, this variant is classified as benign.
Illumina Clinical Services Laboratory,Illumina RCV000544769 SCV001282723 benign Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-negative 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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