NM_002796.3:c.13T>C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002796.3(PSMB4):c.13T>C(p.Leu5Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000048 in 1,459,566 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
PSMB4
NM_002796.3 synonymous
NM_002796.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.10
Publications
0 publications found
Genes affected
PSMB4 (HGNC:9541): (proteasome 20S subunit beta 4) The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. The core structure is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit. [provided by RefSeq, Jul 2008]
PSMB4 Gene-Disease associations (from GenCC):
- proteasome-associated autoinflammatory syndrome 3Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 1-151399600-T-C is Benign according to our data. Variant chr1-151399600-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 1614478.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.1 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002796.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PSMB4 | NM_002796.3 | MANE Select | c.13T>C | p.Leu5Leu | synonymous | Exon 1 of 7 | NP_002787.2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PSMB4 | ENST00000290541.7 | TSL:1 MANE Select | c.13T>C | p.Leu5Leu | synonymous | Exon 1 of 7 | ENSP00000290541.6 | P28070 | |
| PSMB4 | ENST00000933662.1 | c.13T>C | p.Leu5Leu | synonymous | Exon 1 of 6 | ENSP00000603721.1 | |||
| PSMB4 | ENST00000933663.1 | c.13T>C | p.Leu5Leu | synonymous | Exon 1 of 6 | ENSP00000603722.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459566Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 726162 show subpopulations
GnomAD4 exome
AF:
AC:
7
AN:
1459566
Hom.:
Cov.:
30
AF XY:
AC XY:
4
AN XY:
726162
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33286
American (AMR)
AF:
AC:
0
AN:
43976
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26048
East Asian (EAS)
AF:
AC:
0
AN:
39688
South Asian (SAS)
AF:
AC:
0
AN:
86064
European-Finnish (FIN)
AF:
AC:
0
AN:
53392
Middle Eastern (MID)
AF:
AC:
0
AN:
5734
European-Non Finnish (NFE)
AF:
AC:
6
AN:
1111094
Other (OTH)
AF:
AC:
1
AN:
60284
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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