NM_004233.4:c.154-2135C>T

Variant names:

• chr6-14129385-C-T
• rs11758033
• NM_004233.4:c.154-2135C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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 (AMR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD83	NM_004233.4	c.154-2135C>T		intron_variant	Intron 2 of 4	ENST00000379153.4	NP_004224.1
CD83	NM_001040280.3	c.154-2135C>T		intron_variant	Intron 2 of 4		NP_001035370.1
CD83	NM_001251901.1	c.-24-2135C>T		intron_variant	Intron 2 of 4		NP_001238830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD83	ENST00000379153.4	c.154-2135C>T		intron_variant	Intron 2 of 4	1	NM_004233.4	ENSP00000368450.3
CD83	ENST00000612003.5	c.-24-2135C>T		intron_variant	Intron 2 of 4	4		ENSP00000480760.1

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

African (AFR) AF: 0.0337 AC: 1397 AN: 41514

American (AMR) AF: 0.191 AC: 2912 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3466

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5166

South Asian (SAS) AF: 0.0962 AC: 464 AN: 4822

European-Finnish (FIN) AF: 0.187 AC: 1977 AN: 10546

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10217 AN: 67972

Other (OTH) AF: 0.155 AC: 327 AN: 2106

Alfa AF: 0.141 Hom.: 955

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
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11758033; hg19: chr6-14129616;