rs853358

chr6-14131013-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004233.4(CD83):c.154-507A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,158 control chromosomes in the GnomAD database, including 8,228 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 0.31 (8228 hom., cov: 33)
• Consequence: CD83 NM_004233.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

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 (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD83	NM_004233.4	c.154-507A>T		intron_variant		ENST00000379153.4
CD83	NM_001040280.3	c.154-507A>T		intron_variant
CD83	NM_001251901.1	c.-24-507A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD83	ENST00000379153.4	c.154-507A>T		intron_variant		1	NM_004233.4	P1
CD83	ENST00000612003.4	c.-24-507A>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46619 AN: 152042 Hom.: 8202 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.307 AC: 46687 AN: 152158 Hom.: 8228 Cov.: 33 AF XY: 0.310 AC XY: 23094 AN XY: 74394

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.275

Alfa AF: 0.277 Hom.: 796

Bravo AF: 0.311

Asia WGS AF: 0.330 AC: 1151 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	0.87
Dann	Benign	0.56

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: rs853358; hg19: chr6-14131244;