NM_004233.4:c.207G>A

Variant names:

• chr6-14131573-G-A
• rs7743206
• NM_004233.4:c.207G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_004233.4(CD83):​c.207G>A​(p.Arg69Arg) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 14 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004233.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD83	NM_004233.4	MANE Select	c.207G>A	p.Arg69Arg	synonymous	Exon 3 of 5	NP_004224.1	Q01151
	CD83	NM_001040280.3		c.207G>A	p.Arg69Arg	synonymous	Exon 3 of 5	NP_001035370.1
	CD83	NM_001251901.1		c.30G>A	p.Arg10Arg	synonymous	Exon 3 of 5	NP_001238830.1	A0A087WX61

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD83	ENST00000379153.4	TSL:1 MANE Select	c.207G>A	p.Arg69Arg	synonymous	Exon 3 of 5	ENSP00000368450.3	Q01151
	CD83	ENST00000857144.1		c.207G>A	p.Arg69Arg	synonymous	Exon 3 of 5	ENSP00000527203.1
	CD83	ENST00000612003.5	TSL:4	c.30G>A	p.Arg10Arg	synonymous	Exon 3 of 5	ENSP00000480760.1	A0A087WX61

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19441 AN: 152032 Hom.: 1309 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0700

Gnomad FIN AF: 0.0669

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.116

GnomAD2 exomes AF: 0.117 AC: 29527 AN: 251472 AF XY: 0.115

Gnomad AFR exome AF: 0.142

Gnomad AMR exome AF: 0.0862

Gnomad ASJ exome AF: 0.110

Gnomad EAS exome AF: 0.162

Gnomad FIN exome AF: 0.0712

Gnomad NFE exome AF: 0.138

Gnomad OTH exome AF: 0.119

GnomAD4 exome AF: 0.134 AC: 195607 AN: 1461706 Hom.: 13624 Cov.: 32 AF XY: 0.131 AC XY: 95342 AN XY: 727164

African (AFR) AF: 0.140 AC: 4688 AN: 33476

American (AMR) AF: 0.0879 AC: 3930 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 2798 AN: 26136

East Asian (EAS) AF: 0.146 AC: 5779 AN: 39696

South Asian (SAS) AF: 0.0744 AC: 6421 AN: 86256

European-Finnish (FIN) AF: 0.0740 AC: 3952 AN: 53418

Middle Eastern (MID) AF: 0.0905 AC: 522 AN: 5768

European-Non Finnish (NFE) AF: 0.144 AC: 159569 AN: 1111836

Other (OTH) AF: 0.132 AC: 7948 AN: 60396

GnomAD4 genome AF: 0.128 AC: 19456 AN: 152150 Hom.: 1314 Cov.: 32 AF XY: 0.124 AC XY: 9193 AN XY: 74388

African (AFR) AF: 0.140 AC: 5826 AN: 41494

American (AMR) AF: 0.102 AC: 1559 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3470

East Asian (EAS) AF: 0.160 AC: 827 AN: 5180

South Asian (SAS) AF: 0.0693 AC: 334 AN: 4822

European-Finnish (FIN) AF: 0.0669 AC: 709 AN: 10594

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9500 AN: 67980

Other (OTH) AF: 0.116 AC: 244 AN: 2108

Alfa AF: 0.134 Hom.: 2775

Bravo AF: 0.134

Asia WGS AF: 0.115 AC: 400 AN: 3478

EpiCase AF: 0.139

EpiControl AF: 0.135

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.45
DANN	Benign	0.55
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7743206; hg19: chr6-14131804; COSMIC: COSV64787538;