rs9230

Variant names:

• chr6-14136783-T-C
• rs9230
• NM_004233.4:c.*1547T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.94).
• 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 rank	MANE	Protein	UniProt
CD83	NM_004233.4	c.*1547T>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000379153.4	NP_004224.1
CD83	NM_001040280.3	c.*1547T>C		3_prime_UTR_variant	Exon 5 of 5		NP_001035370.1
CD83	NM_001251901.1	c.*1547T>C		3_prime_UTR_variant	Exon 5 of 5		NP_001238830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD83	ENST00000379153.4	c.*1547T>C		3_prime_UTR_variant	Exon 5 of 5	1	NM_004233.4	ENSP00000368450.3
CD83	ENST00000612003.5	c.*1547T>C		3_prime_UTR_variant	Exon 5 of 5	4		ENSP00000480760.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.778 AC: 32258 AN: 41466

American (AMR) AF: 0.740 AC: 11306 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2527 AN: 3472

East Asian (EAS) AF: 0.822 AC: 4254 AN: 5174

South Asian (SAS) AF: 0.854 AC: 4119 AN: 4822

European-Finnish (FIN) AF: 0.702 AC: 7410 AN: 10556

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52422 AN: 67992

Other (OTH) AF: 0.727 AC: 1537 AN: 2114

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
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: rs9230; hg19: chr6-14137014;