rs3799925

Positions:

• chr6-14127946-C-G
• chr6-14127946-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.154-3574C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,136 control chromosomes in the GnomAD database, including 23,982 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 0.55 (23982 hom., cov: 33)
• Consequence: CD83 NM_004233.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD83	NM_004233.4	c.154-3574C>G		intron_variant		ENST00000379153.4	NP_004224.1
CD83	NM_001040280.3	c.154-3574C>G		intron_variant			NP_001035370.1
CD83	NM_001251901.1	c.-24-3574C>G		intron_variant			NP_001238830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD83	ENST00000379153.4	c.154-3574C>G		intron_variant		1	NM_004233.4	ENSP00000368450.3
CD83	ENST00000612003.4	c.-24-3574C>G		intron_variant		4		ENSP00000480760.1

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83190 AN: 152018 Hom.: 23955 Cov.: 33

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.547 AC: 83279 AN: 152136 Hom.: 23982 Cov.: 33 AF XY: 0.544 AC XY: 40455 AN XY: 74362

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.570

Alfa AF: 0.339 Hom.: 766

Bravo AF: 0.554

Asia WGS AF: 0.416 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.2
DANN	Benign	0.58

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: rs3799925; hg19: chr6-14128177;