Genetic Variant CD83:c.*906A>G (chr6-14136142-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004233.4(CD83):c.*906A>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 0.185 in 152,252 control chromosomes in the GnomAD database, including 3,295 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 0.19 ( 3295 hom., cov: 33)

Exomes 𝑓: 0.20 ( 0 hom. )

Consequence

CD83
NM_004233.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.799

Publications

14 publications found

Variant links:

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]

CD83 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004233.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD83	NM_004233.4	MANE Select	c.*906A>G	3_prime_UTR	Exon 5 of 5	NP_004224.1
CD83	NM_001040280.3		c.*906A>G	3_prime_UTR	Exon 5 of 5	NP_001035370.1
CD83	NM_001251901.1		c.*906A>G	3_prime_UTR	Exon 5 of 5	NP_001238830.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD83	ENST00000379153.4	TSL:1 MANE Select	c.*906A>G	3_prime_UTR	Exon 5 of 5	ENSP00000368450.3
CD83	ENST00000857144.1		c.*906A>G	3_prime_UTR	Exon 5 of 5	ENSP00000527203.1
CD83	ENST00000612003.5	TSL:4	c.*906A>G	3_prime_UTR	Exon 5 of 5	ENSP00000480760.1

Frequencies

GnomAD3 genomes

AF:

0.185

AC:

28195

AN:

152104

Hom.:

3294

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0680

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.255

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.176

GnomAD4 exome

AF:

0.200

AC:

AN:

Hom.:

Cov.:

AF XY:

0.278

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.231

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.433

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.185

AC:

28192

AN:

152222

Hom.:

3295

Cov.:

AF XY:

0.193

AC XY:

14398

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0681

AC:

2828

AN:

41556

American (AMR)

AF:

0.215

AC:

3291

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

755

AN:

3472

East Asian (EAS)

AF:

0.483

AC:

2496

AN:

5166

South Asian (SAS)

AF:

0.362

AC:

1747

AN:

4828

European-Finnish (FIN)

AF:

0.265

AC:

2810

AN:

10588

Middle Eastern (MID)

AF:

0.240

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.200

AC:

13628

AN:

68010

Other (OTH)

AF:

0.178

AC:

374

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1138

2277

3415

4554

5692

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

330

660

990

1320

1650

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.193

Hom.:

4065

Bravo

AF:

0.176

Asia WGS

AF:

0.363

AC:

1264

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.68

(source)

DANN

Benign

0.39

PhyloP100

-0.80

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over