chr6-14134361-T-C

Position:

• chr6-14134361-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+606T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,208 control chromosomes in the GnomAD database, including 41,727 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 0.74 (41727 hom., cov: 34)
• Consequence: CD83 NM_004233.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD83	NM_004233.4	c.489+606T>C		intron_variant		ENST00000379153.4
CD83	NM_001040280.3	c.489+606T>C		intron_variant
CD83	NM_001251901.1	c.312+606T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD83	ENST00000379153.4	c.489+606T>C		intron_variant		1	NM_004233.4	P1
CD83	ENST00000612003.4	c.312+606T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112461 AN: 152090 Hom.: 41684 Cov.: 34

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.702

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.739 AC: 112554 AN: 152208 Hom.: 41727 Cov.: 34 AF XY: 0.741 AC XY: 55156 AN XY: 74422

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.705

Alfa AF: 0.727 Hom.: 41611

Bravo AF: 0.736

Asia WGS AF: 0.826 AC: 2873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.80
DANN	Benign	0.70

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: rs853360; hg19: chr6-14134592;