GeneBe

ENST00000612003.5:c.*2402A>G

Variant names:

Variant summary

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

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.598

Publications

2 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]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CD83ENST00000612003.5 linkc.*2402A>G 3_prime_UTR_variant Exon 5 of 5 4 ENSP00000480760.1

Frequencies

GnomAD3 genomes
AF:
0.266
AC:
40425
AN:
151986
Hom.:
6849
Cov.:
32
show subpopulations
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
show subpopulations
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1418
2836
4253
5671
7089
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
418
836
1254
1672
2090
<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:
0.312
Hom.:
1031
Bravo
AF:
0.253
Asia WGS
AF:
0.157
AC:
547
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

Other links and lift over

dbSNP: rs10949227; hg19: chr6-14137869; API