rs11758033

chr6-14129385-C-T

Variant summary

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

The NM_004233.4(CD83):c.154-2135C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,074 control chromosomes in the GnomAD database, including 1,418 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 0.12 (1418 hom., cov: 32)
• Consequence: CD83 NM_004233.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD83	NM_004233.4	c.154-2135C>T		intron_variant		ENST00000379153.4
CD83	NM_001040280.3	c.154-2135C>T		intron_variant
CD83	NM_001251901.1	c.-24-2135C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD83	ENST00000379153.4	c.154-2135C>T		intron_variant		1	NM_004233.4	P1
CD83	ENST00000612003.4	c.-24-2135C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17978 AN: 151956 Hom.: 1409 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.118 AC: 17999 AN: 152074 Hom.: 1418 Cov.: 32 AF XY: 0.120 AC XY: 8917 AN XY: 74340

Gnomad4 AFR AF: 0.0337

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.00252

Gnomad4 SAS AF: 0.0962

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.155

Alfa AF: 0.141 Hom.: 864

Bravo AF: 0.116

Asia WGS AF: 0.0530 AC: 185 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	0.15
Dann	Benign	0.63

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: rs11758033; hg19: chr6-14129616;