chr6-14133852-T-C

Position:

• chr6-14133852-T-C

Variant summary

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

The NM_004233.4(CD83):​c.489+97T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 757,554 control chromosomes in the GnomAD database, including 91,611 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 0.46 (16107 hom., cov: 32)
  • Exomes 𝑓: 0.49 (75504 hom.)
• Consequence: CD83 NM_004233.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.10

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD83	NM_004233.4	c.489+97T>C		intron_variant		ENST00000379153.4	NP_004224.1
CD83	NM_001040280.3	c.489+97T>C		intron_variant			NP_001035370.1
CD83	NM_001251901.1	c.312+97T>C		intron_variant			NP_001238830.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD83	ENST00000379153.4	c.489+97T>C		intron_variant		1	NM_004233.4	ENSP00000368450.3
CD83	ENST00000612003.4	c.312+97T>C		intron_variant		4		ENSP00000480760.1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 69367 AN: 150282 Hom.: 16095 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.447

GnomAD4 exome AF: 0.494 AC: 300123 AN: 607154 Hom.: 75504 AF XY: 0.495 AC XY: 157206 AN XY: 317304

Gnomad4 AFR exome AF: 0.394

Gnomad4 AMR exome AF: 0.425

Gnomad4 ASJ exome AF: 0.433

Gnomad4 EAS exome AF: 0.348

Gnomad4 SAS exome AF: 0.504

Gnomad4 FIN exome AF: 0.423

Gnomad4 NFE exome AF: 0.524

Gnomad4 OTH exome AF: 0.493

GnomAD4 genome AF: 0.462 AC: 69421 AN: 150400 Hom.: 16107 Cov.: 32 AF XY: 0.458 AC XY: 33666 AN XY: 73504

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.449

Alfa AF: 0.490 Hom.: 18363

Bravo AF: 0.454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.050
DANN	Benign	0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9296925; hg19: chr6-14134083;