rs7743206
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_004233.4(CD83):c.207G>A(p.Arg69=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,613,856 control chromosomes in the GnomAD database, including 14,938 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 0.13 ( 1314 hom., cov: 32)
Exomes 𝑓: 0.13 ( 13624 hom. )
Consequence
CD83
NM_004233.4 synonymous
NM_004233.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.371
Genes affected
CD83 (HGNC:1703): (CD83 molecule) The protein encoded by this gene is a single-pass type I membrane protein and member of the immunoglobulin superfamily of receptors. The encoded protein may be involved in the regulation of antigen presentation. A soluble form of this protein can bind to dendritic cells and inhibit their maturation. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
Synonymous conserved (PhyloP=-0.371 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD83 | NM_004233.4 | c.207G>A | p.Arg69= | synonymous_variant | 3/5 | ENST00000379153.4 | |
CD83 | NM_001040280.3 | c.207G>A | p.Arg69= | synonymous_variant | 3/5 | ||
CD83 | NM_001251901.1 | c.30G>A | p.Arg10= | synonymous_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD83 | ENST00000379153.4 | c.207G>A | p.Arg69= | synonymous_variant | 3/5 | 1 | NM_004233.4 | P1 | |
CD83 | ENST00000612003.4 | c.30G>A | p.Arg10= | synonymous_variant | 3/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.128 AC: 19441AN: 152032Hom.: 1309 Cov.: 32
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GnomAD3 exomes AF: 0.117 AC: 29527AN: 251472Hom.: 1856 AF XY: 0.115 AC XY: 15576AN XY: 135910
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GnomAD4 exome AF: 0.134 AC: 195607AN: 1461706Hom.: 13624 Cov.: 32 AF XY: 0.131 AC XY: 95342AN XY: 727164
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GnomAD4 genome AF: 0.128 AC: 19456AN: 152150Hom.: 1314 Cov.: 32 AF XY: 0.124 AC XY: 9193AN XY: 74388
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at