rs1235715459
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_002796.3(PSMB4):c.44delG(p.Gly15ValfsTer37) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,396 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
PSMB4
NM_002796.3 frameshift
NM_002796.3 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0280
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]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PSMB4 | NM_002796.3 | c.44delG | p.Gly15ValfsTer37 | frameshift_variant | Exon 1 of 7 | ENST00000290541.7 | NP_002787.2 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461396Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726976 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461396
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
726976
Gnomad4 AFR exome
AF:
AC:
0
AN:
33472
Gnomad4 AMR exome
AF:
AC:
0
AN:
44668
Gnomad4 ASJ exome
AF:
AC:
0
AN:
26116
Gnomad4 EAS exome
AF:
AC:
0
AN:
39684
Gnomad4 SAS exome
AF:
AC:
0
AN:
86208
Gnomad4 FIN exome
AF:
AC:
0
AN:
53390
Gnomad4 NFE exome
AF:
AC:
0
AN:
1111746
Gnomad4 Remaining exome
AF:
AC:
1
AN:
60370
Heterozygous variant carriers
0
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1
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2
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0.95
Allele balance
Exome Het
Variant carriers
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mutation Taster
=14/186
disease causing (fs/PTC)
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