rs1050648

Variant names:

• chr6-14136078-C-T
• rs1050648
• NM_004233.4:c.*842C>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.*842C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 152,298 control chromosomes in the GnomAD database, including 259 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 0.050 (259 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: CD83 NM_004233.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 6 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0707 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD83	NM_004233.4	MANE Select	c.*842C>T		3_prime_UTR	Exon 5 of 5	NP_004224.1
	CD83	NM_001040280.3		c.*842C>T		3_prime_UTR	Exon 5 of 5	NP_001035370.1
	CD83	NM_001251901.1		c.*842C>T		3_prime_UTR	Exon 5 of 5	NP_001238830.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD83	ENST00000379153.4	TSL:1 MANE Select	c.*842C>T		3_prime_UTR	Exon 5 of 5	ENSP00000368450.3
	CD83	ENST00000612003.5	TSL:4	c.*842C>T		3_prime_UTR	Exon 5 of 5	ENSP00000480760.1

Frequencies

GnomAD3 genomes AF: 0.0500 AC: 7600 AN: 152142 Hom.: 259 Cov.: 32

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0430

Gnomad ASJ AF: 0.0675

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0309

Gnomad FIN AF: 0.0881

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0723

Gnomad OTH AF: 0.0656

GnomAD4 exome AF: 0.132 AC: 5 AN: 38 Hom.: 0 Cov.: 0 AF XY: 0.0667 AC XY: 2 AN XY: 30

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.156 AC: 5 AN: 32

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0499 AC: 7600 AN: 152260 Hom.: 259 Cov.: 32 AF XY: 0.0499 AC XY: 3713 AN XY: 74438

African (AFR) AF: 0.0125 AC: 519 AN: 41546

American (AMR) AF: 0.0429 AC: 657 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0675 AC: 234 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4824

European-Finnish (FIN) AF: 0.0881 AC: 934 AN: 10600

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0723 AC: 4921 AN: 68028

Other (OTH) AF: 0.0649 AC: 137 AN: 2110

Alfa AF: 0.0566 Hom.: 138

Bravo AF: 0.0458

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.20
DANN	Benign	0.55
PhyloP100		-2.0
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: rs1050648; hg19: chr6-14136309;