Genetic Variant CD83:c.489+97T>C (chr6-14133852-T-C) – 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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.10

Publications

10 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=-0.98).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CD83	NM_004233.4 link	c.489+97T>C	intron_variant	Intron 4 of 4	ENST00000379153.4	NP_004224.1	Q01151
CD83	NM_001040280.3 link	c.489+97T>C	intron_variant	Intron 4 of 4		NP_001035370.1	Q01151
CD83	NM_001251901.1 link	c.312+97T>C	intron_variant	Intron 4 of 4		NP_001238830.1	Q01151A0A087WX61

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD83	ENST00000379153.4 link	c.489+97T>C		intron_variant	Intron 4 of 4	1	NM_004233.4	ENSP00000368450.3		Q01151
CD83	ENST00000612003.5 link	c.312+97T>C		intron_variant	Intron 4 of 4	4		ENSP00000480760.1		A0A087WX61

Frequencies

GnomAD3 genomes

AF:

0.462

AC:

69367

AN:

150282

Hom.:

16095

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.394

AC:

5707

AN:

14486

American (AMR)

AF:

0.425

AC:

10948

AN:

25758

Ashkenazi Jewish (ASJ)

AF:

0.433

AC:

7039

AN:

16246

East Asian (EAS)

AF:

0.348

AC:

11297

AN:

32420

South Asian (SAS)

AF:

0.504

AC:

25304

AN:

50244

European-Finnish (FIN)

AF:

0.423

AC:

16650

AN:

39386

Middle Eastern (MID)

AF:

0.387

AC:

1211

AN:

3130

European-Non Finnish (NFE)

AF:

0.524

AC:

206864

AN:

394862

Other (OTH)

AF:

0.493

AC:

15103

AN:

30622

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

7263

14526

21789

29052

36315

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3186

6372

9558

12744

15930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.462

AC:

69421

AN:

150400

Hom.:

16107

Cov.:

AF XY:

0.458

AC XY:

33666

AN XY:

73504

show subpopulations

African (AFR)

AF:

0.387

AC:

15465

AN:

39934

American (AMR)

AF:

0.449

AC:

6848

AN:

15236

Ashkenazi Jewish (ASJ)

AF:

0.435

AC:

1510

AN:

3468

East Asian (EAS)

AF:

0.395

AC:

2038

AN:

5160

South Asian (SAS)

AF:

0.496

AC:

2392

AN:

4818

European-Finnish (FIN)

AF:

0.407

AC:

4295

AN:

10556

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.520

AC:

35302

AN:

67934

Other (OTH)

AF:

0.449

AC:

939

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1923

3846

5768

7691

9614

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

644

1288

1932

2576

3220

<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:

0.486

Hom.:

23504

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

(source)

DANN

Benign

0.26

PhyloP100

-4.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over