NM_002794.5:c.457C>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002794.5(PSMB2):c.457C>T(p.Arg153Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,612,962 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002794.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMB2 | NM_002794.5 | c.457C>T | p.Arg153Cys | missense_variant | Exon 5 of 6 | ENST00000373237.4 | NP_002785.1 | |
PSMB2 | NM_001199779.2 | c.382C>T | p.Arg128Cys | missense_variant | Exon 5 of 6 | NP_001186708.1 | ||
PSMB2 | NM_001199780.2 | c.106C>T | p.Arg36Cys | missense_variant | Exon 4 of 5 | NP_001186709.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSMB2 | ENST00000373237.4 | c.457C>T | p.Arg153Cys | missense_variant | Exon 5 of 6 | 1 | NM_002794.5 | ENSP00000362334.3 | ||
PSMB2 | ENST00000621781.4 | c.106C>T | p.Arg36Cys | missense_variant | Exon 4 of 5 | 1 | ENSP00000479706.1 | |||
PSMB2 | ENST00000630477.1 | n.345C>T | non_coding_transcript_exon_variant | Exon 4 of 5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250492Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135454
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460664Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 726686
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.457C>T (p.R153C) alteration is located in exon 5 (coding exon 5) of the PSMB2 gene. This alteration results from a C to T substitution at nucleotide position 457, causing the arginine (R) at amino acid position 153 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at