rs3181107
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006139.4(CD28):c.410-645G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 152,214 control chromosomes in the GnomAD database, including 64,253 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 0.92 ( 64253 hom., cov: 31)
Consequence
CD28
NM_006139.4 intron
NM_006139.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0110
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=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD28 | NM_006139.4 | c.410-645G>A | intron_variant | ENST00000324106.9 | |||
CD28 | NM_001243077.2 | c.119-645G>A | intron_variant | ||||
CD28 | NM_001243078.2 | c.53-645G>A | intron_variant | ||||
CD28 | NM_001410981.1 | c.452-645G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD28 | ENST00000324106.9 | c.410-645G>A | intron_variant | 1 | NM_006139.4 | P1 | |||
CD28 | ENST00000374481.7 | c.53-645G>A | intron_variant | 1 | |||||
CD28 | ENST00000458610.6 | c.452-645G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.918 AC: 139678AN: 152096Hom.: 64196 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: 0.918 AC: 139793AN: 152214Hom.: 64253 Cov.: 31 AF XY: 0.921 AC XY: 68543AN XY: 74424
GnomAD4 genome
?
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139793
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68543
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74424
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3347
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3470
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