rs9230

Positions:

• chr6-14136783-T-C
• chr6-14136783-T-G

Variant summary

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

The NM_004233.4(CD83):​c.*1547T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,080 control chromosomes in the GnomAD database, including 44,962 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 0.77 (44962 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CD83 NM_004233.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD83	NM_004233.4	c.*1547T>C		3_prime_UTR_variant	5/5	ENST00000379153.4	NP_004224.1
CD83	NM_001040280.3	c.*1547T>C		3_prime_UTR_variant	5/5		NP_001035370.1
CD83	NM_001251901.1	c.*1547T>C		3_prime_UTR_variant	5/5		NP_001238830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD83	ENST00000379153.4	c.*1547T>C		3_prime_UTR_variant	5/5	1	NM_004233.4	ENSP00000368450	P1
CD83	ENST00000612003.4	c.*1547T>C		3_prime_UTR_variant	5/5	4		ENSP00000480760

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116734 AN: 151962 Hom.: 44939 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.725

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.768 AC: 116808 AN: 152080 Hom.: 44962 Cov.: 32 AF XY: 0.768 AC XY: 57108 AN XY: 74326

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.727

Alfa AF: 0.692 Hom.: 2000

Bravo AF: 0.768

Asia WGS AF: 0.823 AC: 2861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.73

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: rs9230; hg19: chr6-14137014;