ClinVar Miner

Submissions for variant NM_001079.4(ZAP70):c.403-3T>C

gnomAD frequency: 0.00001  dbSNP: rs202193449
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001047967 SCV001211953 uncertain significance ZAP70-Related Severe Combined Immunodeficiency 2021-09-01 criteria provided, single submitter clinical testing This sequence change falls in intron 3 of the ZAP70 gene. It does not directly change the encoded amino acid sequence of the ZAP70 protein. It affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with ZAP70-related conditions. 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 is not likely to affect RNA splicing. 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.
Illumina Laboratory Services, Illumina RCV001141987 SCV001302380 uncertain significance Combined immunodeficiency due to ZAP70 deficiency 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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