rs7743206

chr6-14131573-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• 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]

ACMG classification

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: 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

GnomAD3 exomes AF: 0.117 AC: 29527 AN: 251472 Hom.: 1856 AF XY: 0.115 AC XY: 15576 AN XY: 135910

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 SAS exome AF: 0.0716

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

Gnomad4 AFR exome AF: 0.140

Gnomad4 AMR exome AF: 0.0879

Gnomad4 ASJ exome AF: 0.107

Gnomad4 EAS exome AF: 0.146

Gnomad4 SAS exome AF: 0.0744

Gnomad4 FIN exome AF: 0.0740

Gnomad4 NFE exome AF: 0.144

Gnomad4 OTH exome AF: 0.132

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

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.0693

Gnomad4 FIN AF: 0.0669

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.116

Alfa AF: 0.134 Hom.: 2250

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.45
Dann	Benign	0.55

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

Publications

LitVar

Other links and lift over

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