chr6-14137638-A-G

Variant names:

• chr6-14137638-A-G
• rs10949227
• ENST00000612003.5:c.*2402A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000612003.5(CD83):​c.*2402A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,104 control chromosomes in the GnomAD database, including 6,842 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 0.27 (6842 hom., cov: 32)
• Consequence: CD83 ENST00000612003.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612003.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD83	ENST00000612003.5	TSL:4	c.*2402A>G		3_prime_UTR	Exon 5 of 5	ENSP00000480760.1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40425 AN: 151986 Hom.: 6849 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.266 AC: 40413 AN: 152104 Hom.: 6842 Cov.: 32 AF XY: 0.264 AC XY: 19598 AN XY: 74362

African (AFR) AF: 0.0693 AC: 2878 AN: 41524

American (AMR) AF: 0.298 AC: 4554 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3472

East Asian (EAS) AF: 0.00580 AC: 30 AN: 5174

South Asian (SAS) AF: 0.350 AC: 1689 AN: 4822

European-Finnish (FIN) AF: 0.292 AC: 3085 AN: 10552

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25884 AN: 67964

Other (OTH) AF: 0.277 AC: 584 AN: 2110

Alfa AF: 0.312 Hom.: 1031

Bravo AF: 0.253

Asia WGS AF: 0.157 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.66
PhyloP100		-0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10949227; hg19: chr6-14137869;