2-203729683-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006139.4(CD28):c.445C>T(p.Pro149Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006139.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD28 | NM_006139.4 | c.445C>T | p.Pro149Ser | missense_variant | Exon 3 of 4 | ENST00000324106.9 | NP_006130.1 | |
CD28 | NM_001410981.1 | c.487C>T | p.Pro163Ser | missense_variant | Exon 3 of 4 | NP_001397910.1 | ||
CD28 | NM_001243077.2 | c.154C>T | p.Pro52Ser | missense_variant | Exon 3 of 4 | NP_001230006.1 | ||
CD28 | NM_001243078.2 | c.88C>T | p.Pro30Ser | missense_variant | Exon 2 of 3 | NP_001230007.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD28 | ENST00000324106.9 | c.445C>T | p.Pro149Ser | missense_variant | Exon 3 of 4 | 1 | NM_006139.4 | ENSP00000324890.7 | ||
CD28 | ENST00000458610.6 | c.487C>T | p.Pro163Ser | missense_variant | Exon 3 of 4 | 1 | ENSP00000393648.2 | |||
CD28 | ENST00000374481.7 | c.88C>T | p.Pro30Ser | missense_variant | Exon 2 of 3 | 1 | ENSP00000363605.4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251448Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135896
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461760Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727180
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at