rs1181388
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006139.4(CD28):c.52+4480A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,120 control chromosomes in the GnomAD database, including 49,419 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.80 ( 49419 hom., cov: 31)
Consequence
CD28
NM_006139.4 intron
NM_006139.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0910
Genes affected
CD28 (HGNC:1653): (CD28 molecule) The protein encoded by this gene is essential for T-cell proliferation and survival, cytokine production, and T-helper type-2 development. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD28 | NM_006139.4 | c.52+4480A>G | intron_variant | ENST00000324106.9 | |||
CD28 | NM_001243077.2 | c.52+4480A>G | intron_variant | ||||
CD28 | NM_001243078.2 | c.52+4480A>G | intron_variant | ||||
CD28 | NM_001410981.1 | c.94+4611A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD28 | ENST00000324106.9 | c.52+4480A>G | intron_variant | 1 | NM_006139.4 | P1 | |||
CD28 | ENST00000374481.7 | c.52+4480A>G | intron_variant | 1 | |||||
CD28 | ENST00000458610.6 | c.94+4611A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.802 AC: 121902AN: 152000Hom.: 49407 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.802 AC: 121957AN: 152120Hom.: 49419 Cov.: 31 AF XY: 0.801 AC XY: 59549AN XY: 74366
GnomAD4 genome
?
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121957
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152120
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31
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59549
AN XY:
74366
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Asia WGS
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2500
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at