chr17-38755896-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002795.4(PSMB3):āc.202A>Gā(p.Lys68Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000123 in 1,613,948 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K68N) has been classified as Uncertain significance.
Frequency
Consequence
NM_002795.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMB3 | NM_002795.4 | c.202A>G | p.Lys68Glu | missense_variant | 3/6 | ENST00000619426.5 | |
PSMB3 | NR_104194.2 | n.288A>G | non_coding_transcript_exon_variant | 3/5 | |||
PSMB3 | NR_104195.2 | n.288A>G | non_coding_transcript_exon_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMB3 | ENST00000619426.5 | c.202A>G | p.Lys68Glu | missense_variant | 3/6 | 1 | NM_002795.4 | P1 | |
PSMB3 | ENST00000610434.4 | c.193A>G | p.Lys65Glu | missense_variant | 3/4 | 3 | |||
PSMB3 | ENST00000620309.4 | c.202A>G | p.Lys68Glu | missense_variant, NMD_transcript_variant | 3/5 | 2 | |||
PSMB3 | ENST00000613870.4 | c.202A>G | p.Lys68Glu | missense_variant, NMD_transcript_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152086Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251454Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135900
GnomAD4 exome AF: 0.000131 AC: 192AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.000129 AC XY: 94AN XY: 727236
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152086Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2024 | The c.202A>G (p.K68E) alteration is located in exon 3 (coding exon 3) of the PSMB3 gene. This alteration results from a A to G substitution at nucleotide position 202, causing the lysine (K) at amino acid position 68 to be replaced by a glutamic acid (E). 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