rs3799924

chr6-14128110-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.56).
• 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/exons	MANE	UniProt
CD83	NM_004233.4	c.154-3410T>C		intron_variant		ENST00000379153.4
CD83	NM_001040280.3	c.154-3410T>C		intron_variant
CD83	NM_001251901.1	c.-24-3410T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD83	ENST00000379153.4	c.154-3410T>C		intron_variant		1	NM_004233.4	P1
CD83	ENST00000612003.4	c.-24-3410T>C		intron_variant		4

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

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.309

Alfa AF: 0.279 Hom.: 1655

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

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: rs3799924; hg19: chr6-14128341;