rs853358

Variant names:

• chr6-14131013-A-T
• rs853358
• NM_004233.4:c.154-507A>T

Variant summary

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

The NM_004233.4(CD83):​c.154-507A>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
• Publications: 5 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=-0.83).
• 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 rank	MANE	Protein	UniProt
CD83	NM_004233.4	c.154-507A>T		intron_variant	Intron 2 of 4	ENST00000379153.4	NP_004224.1
CD83	NM_001040280.3	c.154-507A>T		intron_variant	Intron 2 of 4		NP_001035370.1
CD83	NM_001251901.1	c.-24-507A>T		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.154-507A>T		intron_variant	Intron 2 of 4	1	NM_004233.4	ENSP00000368450.3
CD83	ENST00000612003.5	c.-24-507A>T		intron_variant	Intron 2 of 4	4		ENSP00000480760.1

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

African (AFR) AF: 0.479 AC: 19848 AN: 41478

American (AMR) AF: 0.255 AC: 3902 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3472

East Asian (EAS) AF: 0.404 AC: 2091 AN: 5182

South Asian (SAS) AF: 0.328 AC: 1584 AN: 4832

European-Finnish (FIN) AF: 0.300 AC: 3176 AN: 10590

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14176 AN: 67982

Other (OTH) AF: 0.275 AC: 582 AN: 2116

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
PhyloP100		-0.030
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: rs853358; hg19: chr6-14131244;