rs3799924

Variant names:

• chr6-14128110-T-C
• rs3799924
• NM_004233.4:c.154-3410T>C

Variant summary

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

The NM_004233.4(CD83):​c.154-3410T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,118 control chromosomes in the GnomAD database, including 8,571 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 0.30 (8571 hom., cov: 32)
• Consequence: CD83 NM_004233.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819
• Publications: 7 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=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD83	NM_004233.4	c.154-3410T>C		intron_variant	Intron 2 of 4	ENST00000379153.4	NP_004224.1
CD83	NM_001040280.3	c.154-3410T>C		intron_variant	Intron 2 of 4		NP_001035370.1
CD83	NM_001251901.1	c.-24-3410T>C		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.154-3410T>C		intron_variant	Intron 2 of 4	1	NM_004233.4	ENSP00000368450.3
CD83	ENST00000612003.5	c.-24-3410T>C		intron_variant	Intron 2 of 4	4		ENSP00000480760.1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45435 AN: 152000 Hom.: 8548 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.299 AC: 45514 AN: 152118 Hom.: 8571 Cov.: 32 AF XY: 0.297 AC XY: 22077 AN XY: 74364

African (AFR) AF: 0.532 AC: 22053 AN: 41454

American (AMR) AF: 0.289 AC: 4409 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3470

East Asian (EAS) AF: 0.126 AC: 654 AN: 5182

South Asian (SAS) AF: 0.128 AC: 619 AN: 4826

European-Finnish (FIN) AF: 0.244 AC: 2581 AN: 10594

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13431 AN: 67998

Other (OTH) AF: 0.309 AC: 652 AN: 2108

Alfa AF: 0.284 Hom.: 1752

Bravo AF: 0.314

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	20
DANN	Benign	0.82
PhyloP100		0.82
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: rs3799924; hg19: chr6-14128341;