rs853366

Variant names:

• chr6-14140920-G-C
• rs853366
• ENST00000612003.5:c.*5684G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000612003.5(CD83):​c.*5684G>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,132 control chromosomes in the GnomAD database, including 4,556 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 0.23 (4556 hom., cov: 31)
• Consequence: CD83 ENST00000612003.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• Publications: 2 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD83	ENST00000612003.5	c.*5684G>C		downstream_gene_variant		4		ENSP00000480760.1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35572 AN: 152012 Hom.: 4542 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.259

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.234 AC: 35643 AN: 152132 Hom.: 4556 Cov.: 31 AF XY: 0.233 AC XY: 17358 AN XY: 74378

African (AFR) AF: 0.326 AC: 13534 AN: 41472

American (AMR) AF: 0.247 AC: 3771 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3472

East Asian (EAS) AF: 0.0862 AC: 447 AN: 5184

South Asian (SAS) AF: 0.118 AC: 571 AN: 4824

European-Finnish (FIN) AF: 0.250 AC: 2647 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12983 AN: 67994

Other (OTH) AF: 0.257 AC: 544 AN: 2114

Alfa AF: 0.220 Hom.: 505

Bravo AF: 0.240

Asia WGS AF: 0.131 AC: 458 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.15
DANN	Benign	0.62
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs853366; hg19: chr6-14141151;