chr12-6816241-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001195015.3(CD4):c.-27C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 1,614,120 control chromosomes in the GnomAD database, including 1,611 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001195015.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD4 | NM_000616.5 | c.793C>T | p.Arg265Trp | missense_variant | Exon 6 of 10 | ENST00000011653.9 | NP_000607.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0596 AC: 9064AN: 152120Hom.: 831 Cov.: 32
GnomAD3 exomes AF: 0.0191 AC: 4780AN: 250838Hom.: 358 AF XY: 0.0151 AC XY: 2050AN XY: 135646
GnomAD4 exome AF: 0.00851 AC: 12438AN: 1461882Hom.: 777 Cov.: 34 AF XY: 0.00779 AC XY: 5664AN XY: 727242
GnomAD4 genome AF: 0.0597 AC: 9083AN: 152238Hom.: 834 Cov.: 32 AF XY: 0.0580 AC XY: 4318AN XY: 74442
ClinVar
Submissions by phenotype
Okt4 epitope deficiency Pathogenic:1Benign:1
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. -
- -
not specified Benign:1
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. -
CD4-related disorder Benign:1
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). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at