chr6-143462894-AT-A
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_003630.3(PEX3):c.206-14del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.69 ( 36245 hom., cov: 0)
Exomes 𝑓: 0.64 ( 292704 hom. )
Consequence
PEX3
NM_003630.3 intron
NM_003630.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0500
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 -16 ACMG points.
BP6
Variant 6-143462894-AT-A is Benign according to our data. Variant chr6-143462894-AT-A is described in ClinVar as [Benign]. Clinvar id is 259105.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-143462894-AT-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX3 | NM_003630.3 | c.206-14del | intron_variant | ENST00000367591.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX3 | ENST00000367591.5 | c.206-14del | intron_variant | 1 | NM_003630.3 | P1 | |||
PEX3 | ENST00000367592.5 | c.74-14del | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.687 AC: 104205AN: 151652Hom.: 36192 Cov.: 0
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GnomAD3 exomes AF: 0.650 AC: 163046AN: 250758Hom.: 53805 AF XY: 0.639 AC XY: 86558AN XY: 135564
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GnomAD4 exome AF: 0.636 AC: 911409AN: 1433936Hom.: 292704 Cov.: 0 AF XY: 0.632 AC XY: 452098AN XY: 715350
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GnomAD4 genome AF: 0.687 AC: 104314AN: 151768Hom.: 36245 Cov.: 0 AF XY: 0.687 AC XY: 50975AN XY: 74180
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Peroxisome biogenesis disorder 10B Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Peroxisome biogenesis disorder 10A (Zellweger) Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2022 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at