chr8-76983806-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000318.3(PEX2):c.373C>A(p.Arg125=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000137 in 1,461,828 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 (★). Synonymous variant affecting the same amino acid position (i.e. R125R) has been classified as Likely benign.
Frequency
Consequence
NM_000318.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX2 | NM_000318.3 | c.373C>A | p.Arg125= | synonymous_variant | 4/4 | ENST00000357039.9 | |
PEX2 | NM_001079867.2 | c.373C>A | p.Arg125= | synonymous_variant | 3/3 | ||
PEX2 | NM_001172086.2 | c.373C>A | p.Arg125= | synonymous_variant | 5/5 | ||
PEX2 | NM_001172087.2 | c.373C>A | p.Arg125= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX2 | ENST00000357039.9 | c.373C>A | p.Arg125= | synonymous_variant | 4/4 | 1 | NM_000318.3 | P1 | |
PEX2 | ENST00000522527.5 | c.373C>A | p.Arg125= | synonymous_variant | 3/3 | 1 | P1 | ||
PEX2 | ENST00000520103.5 | c.373C>A | p.Arg125= | synonymous_variant | 3/3 | 2 | P1 | ||
PEX2 | ENST00000518986.5 | c.373C>A | p.Arg125= | synonymous_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251382Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135868
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461828Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727202
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Peroxisome biogenesis disorder 5A (Zellweger) Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 10, 2021 | This variant has not been reported in the literature in individuals affected with PEX2-related conditions. This variant is present in population databases (rs61752124, ExAC 0.006%). This sequence change affects codon 125 of the PEX2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the PEX2 protein. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at