rs6929821

chr6-14126191-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.154-5329T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,078 control chromosomes in the GnomAD database, including 4,867 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 0.25 (4867 hom., cov: 32)
• Consequence: CD83 NM_004233.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD83	NM_004233.4	c.154-5329T>C		intron_variant		ENST00000379153.4
CD83	NM_001040280.3	c.154-5329T>C		intron_variant
CD83	NM_001251901.1	c.-24-5329T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD83	ENST00000379153.4	c.154-5329T>C		intron_variant		1	NM_004233.4	P1
CD83	ENST00000612003.4	c.-24-5329T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37730 AN: 151960 Hom.: 4872 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.248 AC: 37741 AN: 152078 Hom.: 4867 Cov.: 32 AF XY: 0.247 AC XY: 18365 AN XY: 74320

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.261

Alfa AF: 0.270 Hom.: 11654

Bravo AF: 0.241

Asia WGS AF: 0.240 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	8.7
Dann	Benign	0.38

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: rs6929821; hg19: chr6-14126422;