1-10506158-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_004565.3(PEX14):​c.84+10837A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,076 control chromosomes in the GnomAD database, including 6,474 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.27 ( 6474 hom., cov: 33)

Consequence

PEX14
NM_004565.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.136
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 1-10506158-A-G is Benign according to our data. Variant chr1-10506158-A-G is described in ClinVar as [Benign]. Clinvar id is 225769.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PEX14NM_004565.3 linkc.84+10837A>G intron_variant Intron 2 of 8 ENST00000356607.9 NP_004556.1 O75381-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PEX14ENST00000356607.9 linkc.84+10837A>G intron_variant Intron 2 of 8 1 NM_004565.3 ENSP00000349016.4 O75381-1
PEX14ENST00000491661.2 linkc.69+10837A>G intron_variant Intron 2 of 5 2 ENSP00000465473.1 K7EK59
PEX14ENST00000472851.1 linkn.341+10837A>G intron_variant Intron 2 of 3 3

Frequencies

GnomAD3 genomes
AF:
0.274
AC:
41694
AN:
151958
Hom.:
6472
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.124
Gnomad AMI
AF:
0.379
Gnomad AMR
AF:
0.373
Gnomad ASJ
AF:
0.277
Gnomad EAS
AF:
0.326
Gnomad SAS
AF:
0.243
Gnomad FIN
AF:
0.336
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.331
Gnomad OTH
AF:
0.294
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.274
AC:
41696
AN:
152076
Hom.:
6474
Cov.:
33
AF XY:
0.274
AC XY:
20389
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.124
Gnomad4 AMR
AF:
0.373
Gnomad4 ASJ
AF:
0.277
Gnomad4 EAS
AF:
0.326
Gnomad4 SAS
AF:
0.241
Gnomad4 FIN
AF:
0.336
Gnomad4 NFE
AF:
0.331
Gnomad4 OTH
AF:
0.291
Alfa
AF:
0.321
Hom.:
11753
Bravo
AF:
0.276
Asia WGS
AF:
0.286
AC:
995
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Peroxisome biogenesis disorder, complementation group K Benign:1
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
3.3
DANN
Benign
0.55

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs616488; hg19: chr1-10566215; API