chr1-10618431-A-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004565.3(PEX14):c.384+14A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 1,599,916 control chromosomes in the GnomAD database, including 18,358 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.19 ( 3289 hom., cov: 33)
Exomes 𝑓: 0.14 ( 15069 hom. )
Consequence
PEX14
NM_004565.3 intron
NM_004565.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.520
Genes affected
PEX14 (HGNC:8856): (peroxisomal biogenesis factor 14) This gene encodes an essential component of the peroxisomal import machinery. The protein is integrated into peroxisome membranes with its C-terminus exposed to the cytosol, and interacts with the cytosolic receptor for proteins containing a PTS1 peroxisomal targeting signal. The protein also functions as a transcriptional corepressor and interacts with a histone deacetylase. A mutation in this gene results in one form of Zellweger syndrome. [provided by RefSeq, Jul 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=-0.82).
BP6
Variant 1-10618431-A-T is Benign according to our data. Variant chr1-10618431-A-T is described in ClinVar as [Benign]. Clinvar id is 95145.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-10618431-A-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX14 | NM_004565.3 | c.384+14A>T | intron_variant | ENST00000356607.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX14 | ENST00000356607.9 | c.384+14A>T | intron_variant | 1 | NM_004565.3 | P1 | |||
PEX14 | ENST00000491661.2 | c.369+14A>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.190 AC: 28931AN: 152152Hom.: 3269 Cov.: 33
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GnomAD3 exomes AF: 0.155 AC: 38508AN: 248840Hom.: 3471 AF XY: 0.157 AC XY: 21089AN XY: 134738
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GnomAD4 exome AF: 0.137 AC: 198517AN: 1447646Hom.: 15069 Cov.: 28 AF XY: 0.139 AC XY: 100463AN XY: 721146
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GnomAD4 genome AF: 0.190 AC: 28992AN: 152270Hom.: 3289 Cov.: 33 AF XY: 0.196 AC XY: 14596AN XY: 74466
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 30, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 26, 2018 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 26, 2015 | - - |
Peroxisome biogenesis disorder, complementation group K Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Peroxisome biogenesis disorder 13A (Zellweger) Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at