rs853361

Variant names:

• chr6-14137907-C-T
• rs853361
• ENST00000612003.5:c.*2671C>T

Variant summary

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

The ENST00000612003.5(CD83):​c.*2671C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,178 control chromosomes in the GnomAD database, including 42,890 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 0.75 (42890 hom., cov: 33)
• Consequence: CD83 ENST00000612003.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.799 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.*2671C>T		3_prime_UTR_variant	Exon 5 of 5	4		ENSP00000480760.1

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113411 AN: 152060 Hom.: 42844 Cov.: 33

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.746 AC: 113518 AN: 152178 Hom.: 42890 Cov.: 33 AF XY: 0.737 AC XY: 54852 AN XY: 74394

African (AFR) AF: 0.721 AC: 29934 AN: 41510

American (AMR) AF: 0.732 AC: 11197 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2610 AN: 3472

East Asian (EAS) AF: 0.356 AC: 1842 AN: 5176

South Asian (SAS) AF: 0.584 AC: 2814 AN: 4816

European-Finnish (FIN) AF: 0.744 AC: 7870 AN: 10584

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54717 AN: 68010

Other (OTH) AF: 0.729 AC: 1542 AN: 2116

Alfa AF: 0.783 Hom.: 10610

Bravo AF: 0.744

Asia WGS AF: 0.491 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.57
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs853361; hg19: chr6-14138138;