ClinVar Miner

Submissions for variant NM_001250.6(CD40):c.647-3dup

dbSNP: rs749590513
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001264503 SCV001442689 benign not specified 2020-10-13 criteria provided, single submitter clinical testing Variant summary: CD40 c.647-3dupT alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.083 in 89320 control chromosomes in the gnomAD database, including 639 homozygotes. The observed variant frequency is approximately 528-fold of the estimated maximal expected allele frequency for a pathogenic variant in CD40 causing Hyper IgM Syndrome Type 3 phenotype (0.00016), strongly suggesting that the variant is benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign.
Genome-Nilou Lab RCV001420684 SCV001623025 benign Hyper-IgM syndrome type 3 2021-05-18 criteria provided, single submitter clinical testing
GeneDx RCV001655709 SCV001864624 benign not provided 2021-06-19 criteria provided, single submitter clinical testing

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