chr14-23026166-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002797.5(PSMB5):c.715C>T(p.Arg239Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,613,974 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R239Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_002797.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMB5 | NM_002797.5 | c.715C>T | p.Arg239Trp | missense_variant | 3/3 | ENST00000361611.11 | |
PSMB5 | NM_001130725.1 | c.406C>T | p.Arg136Trp | missense_variant | 3/3 | ||
PSMB5 | NM_001144932.3 | c.*188C>T | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMB5 | ENST00000361611.11 | c.715C>T | p.Arg239Trp | missense_variant | 3/3 | 1 | NM_002797.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251482Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135916
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461894Hom.: 0 Cov.: 32 AF XY: 0.0000495 AC XY: 36AN XY: 727248
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2022 | The c.715C>T (p.R239W) alteration is located in exon 3 (coding exon 3) of the PSMB5 gene. This alteration results from a C to T substitution at nucleotide position 715, causing the arginine (R) at amino acid position 239 to be replaced by a tryptophan (W). 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