rs17354216

Variant names:

• chr6-14139472-T-C
• rs17354216
• ENST00000612003.5:c.*4236T>C

Variant summary

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

The ENST00000612003.5(CD83):​c.*4236T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.064 in 152,302 control chromosomes in the GnomAD database, including 351 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 0.064 (351 hom., cov: 32)
• Consequence: CD83 ENST00000612003.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 5 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 = 0.0721 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.*4236T>C		3_prime_UTR_variant	Exon 5 of 5	4		ENSP00000480760.1

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9711 AN: 152184 Hom.: 346 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0585

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0640 AC: 9740 AN: 152302 Hom.: 351 Cov.: 32 AF XY: 0.0651 AC XY: 4849 AN XY: 74466

African (AFR) AF: 0.0742 AC: 3086 AN: 41564

American (AMR) AF: 0.0731 AC: 1118 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0236 AC: 82 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4824

European-Finnish (FIN) AF: 0.105 AC: 1110 AN: 10606

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0585 AC: 3978 AN: 68034

Other (OTH) AF: 0.0563 AC: 119 AN: 2114

Alfa AF: 0.0609 Hom.: 465

Bravo AF: 0.0641

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.28
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17354216; hg19: chr6-14139703;