chr6-32858467-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_002800.5(PSMB9):c.494G>A(p.Gly165Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000316 in 1,612,902 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002800.5 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 |
---|---|---|---|---|---|---|---|---|
PSMB9 | NM_002800.5 | c.494G>A | p.Gly165Asp | missense_variant | Exon 5 of 6 | ENST00000374859.3 | NP_002791.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000406 AC: 10AN: 246572Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134412
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460736Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726676
GnomAD4 genome AF: 0.000197 AC: 30AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74350
ClinVar
Submissions by phenotype
Proteasome-associated autoinflammatory syndrome 3 Pathogenic:2
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ACMG classification criteria: PS4 supporting, PM1 moderated, PM2 moderated, PM3 supporting, BP4 supporting -
not specified Uncertain:1
Variant summary: PSMB9 c.494G>A (p.Gly165Asp) results in a non-conservative amino acid change in the encoded protein sequence. Two of four in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 1605926 control chromosomes (i.e. 51 carriers), predominantly at a frequency of 0.00061 within the African or African-American subpopulation in the gnomAD database (v4.1 dataset). This frequency is not higher than the estimated maximum expected for a pathogenic variant in PSMB9 causing Proteasome-Associated Autoinflammatory Syndrome 6, allowing no conclusion about variant significance. The variant, c.494G>A, has been reported in the literature in two siblings affected with Proteasome-Associated Autoinflammatory Syndrome 6 (Brehm_2015), who also carried a frameshift variant in PSMB4 (i.e. another proteosome associated gene); authors proposed an additive effect for the variants, suggesting digenic inheritance. Authors also examined patient derived cells and found normal chymotryptic- and tryptic but somewhat reduced caspase-like activity, which was similar to the findings in healthy fibroblasts when silencing mRNA expression of the respective genes (Brehm_2015). However, these data do not allow clear conclusions about variant significance. The following publication have been ascertained in the context of this evaluation (PMID: 26524591). ClinVar contains an entry for this variant (Variation ID: 548995). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at