ClinVar Miner

Submissions for variant NM_000616.5(CD4):c.793C>T (p.Arg265Trp)

gnomAD frequency: 0.06389  dbSNP: rs28919570
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
H3Africa Consortium RCV001777144 SCV002014627 benign not specified 2020-10-28 criteria provided, single submitter research While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.188, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error.
PreventionGenetics, part of Exact Sciences RCV003964810 SCV004794061 benign CD4-related condition 2019-12-20 criteria provided, single submitter clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
OMIM RCV000022781 SCV000044070 pathogenic Okt4 epitope deficiency 1993-09-01 no assertion criteria provided literature only
Reproductive Health Research and Development, BGI Genomics RCV000022781 SCV001142430 benign Okt4 epitope deficiency 2020-01-06 no assertion criteria provided curation NM_000616.4:c.793C>T (p.Arg265Trp) in the gene CD4 was reported as c.867G>A (p.Arg240Trp). Hodge et al reported this variant in a OKT4-Epitope deficiency patient (PMID: 1708753). In addition, Takenaka et al. reported homozygosity of this variant in patients with OKT4 epitope deficiency (PMID: 7689618). It has an allele frequency of 0.201 in African subpopulation in the gnomAD database. 516 homozygous occurrences are observed in the gnomAD database. This evidence suggests the variant to be classified as benign. ACMG/AMP criteria applied: BA1; BS2; PM3_Supporting; PP4.

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