rs3734665

Positions:

• chr6-14136142-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000379153.4(CD83):​c.*906A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,252 control chromosomes in the GnomAD database, including 3,295 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 0.19 (3295 hom., cov: 33)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: CD83 ENST00000379153.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD83	NM_004233.4	c.*906A>G		3_prime_UTR_variant	5/5	ENST00000379153.4	NP_004224.1
CD83	NM_001040280.3	c.*906A>G		3_prime_UTR_variant	5/5		NP_001035370.1
CD83	NM_001251901.1	c.*906A>G		3_prime_UTR_variant	5/5		NP_001238830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD83	ENST00000379153.4	c.*906A>G		3_prime_UTR_variant	5/5	1	NM_004233.4	ENSP00000368450	P1
CD83	ENST00000612003.4	c.*906A>G		3_prime_UTR_variant	5/5	4		ENSP00000480760

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28195 AN: 152104 Hom.: 3294 Cov.: 33

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.200 AC: 6 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.278 AC XY: 5 AN XY: 18

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.231

GnomAD4 genome AF: 0.185 AC: 28192 AN: 152222 Hom.: 3295 Cov.: 33 AF XY: 0.193 AC XY: 14398 AN XY: 74424

Gnomad4 AFR AF: 0.0681

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.178

Alfa AF: 0.203 Hom.: 2278

Bravo AF: 0.176

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.68
DANN	Benign	0.39

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: rs3734665; hg19: chr6-14136373;