rs113104510
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000466.3(PEX1):c.358-11G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000151 in 1,325,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000015 ( 0 hom. )
Consequence
PEX1
NM_000466.3 intron
NM_000466.3 intron
Scores
2
Splicing: ADA: 0.00001241
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.378
Genes affected
PEX1 (HGNC:8850): (peroxisomal biogenesis factor 1) This gene encodes a member of the AAA ATPase family, a large group of ATPases associated with diverse cellular activities. This protein is cytoplasmic but is often anchored to a peroxisomal membrane where it forms a heteromeric complex and plays a role in the import of proteins into peroxisomes and peroxisome biogenesis. Mutations in this gene have been associated with complementation group 1 peroxisomal disorders such as neonatal adrenoleukodystrophy, infantile Refsum disease, and Zellweger syndrome. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PEX1 | NM_000466.3 | c.358-11G>T | intron_variant | Intron 3 of 23 | ENST00000248633.9 | NP_000457.1 | ||
PEX1 | NM_001282677.2 | c.358-11G>T | intron_variant | Intron 3 of 22 | NP_001269606.1 | |||
PEX1 | NM_001282678.2 | c.-267-11G>T | intron_variant | Intron 3 of 23 | NP_001269607.1 | |||
PEX1 | XM_047420472.1 | c.358-11G>T | intron_variant | Intron 3 of 22 | XP_047276428.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PEX1 | ENST00000248633.9 | c.358-11G>T | intron_variant | Intron 3 of 23 | 1 | NM_000466.3 | ENSP00000248633.4 | |||
PEX1 | ENST00000428214.5 | c.358-11G>T | intron_variant | Intron 3 of 22 | 1 | ENSP00000394413.1 | ||||
PEX1 | ENST00000438045.5 | c.273+3836G>T | intron_variant | Intron 2 of 20 | 2 | ENSP00000410438.1 | ||||
PEX1 | ENST00000484913.5 | n.397-11G>T | intron_variant | Intron 3 of 23 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251138Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135748
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GnomAD4 exome AF: 0.00000151 AC: 2AN: 1325446Hom.: 0 Cov.: 21 AF XY: 0.00000300 AC XY: 2AN XY: 667074
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GnomAD4 genome Cov.: 32
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32
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at