rs4907
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002795.4(PSMB3):c.100A>T(p.Met34Leu) variant causes a missense change. The variant allele was found at a frequency of 0.106 in 1,614,070 control chromosomes in the GnomAD database, including 11,826 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002795.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMB3 | NM_002795.4 | c.100A>T | p.Met34Leu | missense_variant | 2/6 | ENST00000619426.5 | |
PSMB3 | NR_104194.2 | n.186A>T | non_coding_transcript_exon_variant | 2/5 | |||
PSMB3 | NR_104195.2 | n.186A>T | non_coding_transcript_exon_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMB3 | ENST00000619426.5 | c.100A>T | p.Met34Leu | missense_variant | 2/6 | 1 | NM_002795.4 | P1 | |
PSMB3 | ENST00000610434.4 | c.91A>T | p.Met31Leu | missense_variant | 2/4 | 3 | |||
PSMB3 | ENST00000620309.4 | c.100A>T | p.Met34Leu | missense_variant, NMD_transcript_variant | 2/5 | 2 | |||
PSMB3 | ENST00000613870.4 | c.100A>T | p.Met34Leu | missense_variant, NMD_transcript_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.107 AC: 16291AN: 152076Hom.: 1276 Cov.: 32
GnomAD3 exomes AF: 0.146 AC: 36724AN: 251328Hom.: 4288 AF XY: 0.135 AC XY: 18299AN XY: 135890
GnomAD4 exome AF: 0.106 AC: 155206AN: 1461876Hom.: 10551 Cov.: 33 AF XY: 0.104 AC XY: 75881AN XY: 727240
GnomAD4 genome AF: 0.107 AC: 16292AN: 152194Hom.: 1275 Cov.: 32 AF XY: 0.112 AC XY: 8346AN XY: 74392
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at