rs3762000
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003630.3(PEX3):c.332-20C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 1,599,828 control chromosomes in the GnomAD database, including 51,960 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.32 ( 8652 hom., cov: 32)
Exomes 𝑓: 0.24 ( 43308 hom. )
Consequence
PEX3
NM_003630.3 intron
NM_003630.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.143
Genes affected
PEX3 (HGNC:8858): (peroxisomal biogenesis factor 3) The product of this gene is involved in peroxisome biosynthesis and integrity. It assembles membrane vesicles before the matrix proteins are translocated. Peroxins (PEXs) are proteins that are essential for the assembly of functional peroxisomes. The peroxisome biogenesis disorders (PBDs) are a group of genetically heterogeneous autosomal recessive, lethal diseases characterized by multiple defects in peroxisome function. The peroxisomal biogenesis disorders are a heterogeneous group with at least 14 complementation groups and with more than 1 phenotype being observed in cases falling into particular complementation groups. Although the clinical features of PBD patients vary, cells from all PBD patients exhibit a defect in the import of one or more classes of peroxisomal matrix proteins into the organelle. Defects in this gene are a cause Zellweger syndrome (ZWS). [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 6-143470941-C-G is Benign according to our data. Variant chr6-143470941-C-G is described in ClinVar as [Benign]. Clinvar id is 167458.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX3 | NM_003630.3 | c.332-20C>G | intron_variant | ENST00000367591.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX3 | ENST00000367591.5 | c.332-20C>G | intron_variant | 1 | NM_003630.3 | P1 | |||
PEX3 | ENST00000367592.5 | c.200-20C>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.316 AC: 47937AN: 151880Hom.: 8620 Cov.: 32
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GnomAD3 exomes AF: 0.269 AC: 67245AN: 249884Hom.: 9781 AF XY: 0.263 AC XY: 35590AN XY: 135156
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GnomAD4 exome AF: 0.237 AC: 343126AN: 1447830Hom.: 43308 Cov.: 29 AF XY: 0.237 AC XY: 171067AN XY: 721102
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GnomAD4 genome ? AF: 0.316 AC: 48016AN: 151998Hom.: 8652 Cov.: 32 AF XY: 0.318 AC XY: 23641AN XY: 74290
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 21, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 11, 2018 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 19, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at