rs1050648

chr6-14136078-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD83	NM_004233.4	c.*842C>T		3_prime_UTR_variant	5/5	ENST00000379153.4
CD83	NM_001040280.3	c.*842C>T		3_prime_UTR_variant	5/5
CD83	NM_001251901.1	c.*842C>T		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD83	ENST00000379153.4	c.*842C>T		3_prime_UTR_variant	5/5	1	NM_004233.4	P1
CD83	ENST00000612003.4	c.*842C>T		3_prime_UTR_variant	5/5	4

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

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.156

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

Gnomad4 AFR AF: 0.0125

Gnomad4 AMR AF: 0.0429

Gnomad4 ASJ AF: 0.0675

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.0881

Gnomad4 NFE AF: 0.0723

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0625 Hom.: 74

Bravo AF: 0.0458

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.20
Dann	Benign	0.55

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: rs1050648; hg19: chr6-14136309;