rs4715877

Variant names:

• chr6-14130802-G-A
• rs4715877
• NM_004233.4:c.154-718G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-14130802-G-A
• chr6-14130802-G-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.154-718G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,234 control chromosomes in the GnomAD database, including 4,102 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 0.21 (4102 hom., cov: 33)
• Consequence: CD83 NM_004233.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004233.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD83	NM_004233.4	MANE Select	c.154-718G>A		intron	N/A	NP_004224.1
	CD83	NM_001040280.3		c.154-718G>A		intron	N/A	NP_001035370.1
	CD83	NM_001251901.1		c.-24-718G>A		intron	N/A	NP_001238830.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD83	ENST00000379153.4	TSL:1 MANE Select	c.154-718G>A		intron	N/A	ENSP00000368450.3
	CD83	ENST00000857144.1		c.154-718G>A		intron	N/A	ENSP00000527203.1
	CD83	ENST00000612003.5	TSL:4	c.-24-718G>A		intron	N/A	ENSP00000480760.1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31418 AN: 152116 Hom.: 4104 Cov.: 33

Gnomad AFR AF: 0.0700

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.206 AC: 31419 AN: 152234 Hom.: 4102 Cov.: 33 AF XY: 0.202 AC XY: 15061 AN XY: 74442

African (AFR) AF: 0.0699 AC: 2906 AN: 41562

American (AMR) AF: 0.185 AC: 2824 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3468

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5190

South Asian (SAS) AF: 0.175 AC: 846 AN: 4828

European-Finnish (FIN) AF: 0.234 AC: 2483 AN: 10592

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20548 AN: 67990

Other (OTH) AF: 0.215 AC: 455 AN: 2114

Alfa AF: 0.203 Hom.: 1135

Bravo AF: 0.196

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.45
PhyloP100		0.63
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: rs4715877; hg19: chr6-14131033;