rs75899942
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006139.4(CD28):c.272G>A(p.Gly91Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,614,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_006139.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD28 | NM_006139.4 | c.272G>A | p.Gly91Asp | missense_variant | Exon 2 of 4 | ENST00000324106.9 | NP_006130.1 | |
CD28 | NM_001410981.1 | c.314G>A | p.Gly105Asp | missense_variant | Exon 2 of 4 | NP_001397910.1 | ||
CD28 | NM_001243077.2 | c.118+154G>A | intron_variant | Intron 2 of 3 | NP_001230006.1 | |||
CD28 | NM_001243078.2 | c.53-2796G>A | intron_variant | Intron 1 of 2 | NP_001230007.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD28 | ENST00000324106.9 | c.272G>A | p.Gly91Asp | missense_variant | Exon 2 of 4 | 1 | NM_006139.4 | ENSP00000324890.7 | ||
CD28 | ENST00000458610.6 | c.314G>A | p.Gly105Asp | missense_variant | Exon 2 of 4 | 1 | ENSP00000393648.2 | |||
CD28 | ENST00000374481.7 | c.53-2796G>A | intron_variant | Intron 1 of 2 | 1 | ENSP00000363605.4 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251172Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135780
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461782Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727208
GnomAD4 genome AF: 0.000204 AC: 31AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74442
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at