chr17-35575211-TAA-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_000286.3(PEX12):c.*569_*570del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0325 in 154,756 control chromosomes in the GnomAD database, including 101 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.033 ( 100 hom., cov: 32)
Exomes 𝑓: 0.031 ( 1 hom. )
Consequence
PEX12
NM_000286.3 3_prime_UTR
NM_000286.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0580
Genes affected
PEX12 (HGNC:8854): (peroxisomal biogenesis factor 12) This gene belongs to the peroxin-12 family. 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 of Zellweger syndrome (ZWS). [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 17-35575211-TAA-T is Benign according to our data. Variant chr17-35575211-TAA-T is described in ClinVar as [Likely_benign]. Clinvar id is 322640.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0325 (4947/152078) while in subpopulation SAS AF= 0.0529 (255/4816). AF 95% confidence interval is 0.0476. There are 100 homozygotes in gnomad4. There are 2373 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 98 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX12 | NM_000286.3 | c.*569_*570del | 3_prime_UTR_variant | 3/3 | ENST00000225873.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX12 | ENST00000225873.9 | c.*569_*570del | 3_prime_UTR_variant | 3/3 | 1 | NM_000286.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0325 AC: 4937AN: 151958Hom.: 98 Cov.: 32
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GnomAD4 exome AF: 0.0306 AC: 82AN: 2678Hom.: 1 AF XY: 0.0309 AC XY: 44AN XY: 1424
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GnomAD4 genome ? AF: 0.0325 AC: 4947AN: 152078Hom.: 100 Cov.: 32 AF XY: 0.0319 AC XY: 2373AN XY: 74330
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Peroxisome biogenesis disorder 1A (Zellweger) Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
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