rs9370729

Variant names:

• chr6-14138061-C-T
• rs9370729
• ENST00000612003.5:c.*2825C>T

Variant summary

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

The ENST00000612003.5(CD83):​c.*2825C>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 0.439 in 152,006 control chromosomes in the GnomAD database, including 17,380 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 0.44 (17380 hom., cov: 32)
• Consequence: CD83 ENST00000612003.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 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.*2825C>T		3_prime_UTR_variant	Exon 5 of 5	4		ENSP00000480760.1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66803 AN: 151888 Hom.: 17391 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.439 AC: 66797 AN: 152006 Hom.: 17380 Cov.: 32 AF XY: 0.435 AC XY: 32300 AN XY: 74278

African (AFR) AF: 0.165 AC: 6833 AN: 41462

American (AMR) AF: 0.463 AC: 7075 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1625 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1010 AN: 5176

South Asian (SAS) AF: 0.444 AC: 2138 AN: 4810

European-Finnish (FIN) AF: 0.493 AC: 5206 AN: 10550

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41312 AN: 67950

Other (OTH) AF: 0.429 AC: 906 AN: 2110

Alfa AF: 0.543 Hom.: 29752

Bravo AF: 0.423

Asia WGS AF: 0.300 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.42
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9370729; hg19: chr6-14138292;