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.

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	UniProt
CD83	NM_004233.4	MANE Select	c.489+97T>C	intron	N/A	NP_004224.1	Q01151
CD83	NM_001040280.3		c.489+97T>C	intron	N/A	NP_001035370.1
CD83	NM_001251901.1		c.312+97T>C	intron	N/A	NP_001238830.1	A0A087WX61

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD83	ENST00000379153.4	TSL:1 MANE Select	c.489+97T>C	intron	N/A	ENSP00000368450.3	Q01151
CD83	ENST00000857144.1		c.489+97T>C	intron	N/A	ENSP00000527203.1
CD83	ENST00000612003.5	TSL:4	c.312+97T>C	intron	N/A	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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over