Variant 6-143462894-ATT-AT details in Genebe, Genetics Data Aggregator

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

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0500

Variant links:

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]

PEX3 links:

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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 linkuse as main transcript	c.206-14del		intron_variant		ENST00000367591.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PEX3	ENST00000367591.5 linkuse as main transcript	c.206-14del		intron_variant		1	NM_003630.3	P1
PEX3	ENST00000367592.5 linkuse as main transcript	c.74-14del		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.687

AC:

104205

AN:

151652

Hom.:

36192

Cov.:

show subpopulations

Gnomad AFR

AF:

0.780

Gnomad AMI

AF:

0.685

Gnomad AMR

AF:

0.723

Gnomad ASJ

AF:

0.699

Gnomad EAS

AF:

0.552

Gnomad SAS

AF:

0.498

Gnomad FIN

AF:

0.704

Gnomad MID

AF:

0.618

Gnomad NFE

AF:

0.643

Gnomad OTH

AF:

0.679

GnomAD3 exomes

AF:

0.650

AC:

163046

AN:

250758

Hom.:

53805

AF XY:

0.639

AC XY:

86558

AN XY:

135564

show subpopulations

Gnomad AFR exome

AF:

0.782

Gnomad AMR exome

AF:

0.737

Gnomad ASJ exome

AF:

0.694

Gnomad EAS exome

AF:

0.549

Gnomad SAS exome

AF:

0.514

Gnomad FIN exome

AF:

0.697

Gnomad NFE exome

AF:

0.646

Gnomad OTH exome

AF:

0.644

GnomAD4 exome

AF:

0.636

AC:

911409

AN:

1433936

Hom.:

292704

Cov.:

AF XY:

0.632

AC XY:

452098

AN XY:

715350

show subpopulations

Gnomad4 AFR exome

AF:

0.788

Gnomad4 AMR exome

AF:

0.734

Gnomad4 ASJ exome

AF:

0.697

Gnomad4 EAS exome

AF:

0.611

Gnomad4 SAS exome

AF:

0.508

Gnomad4 FIN exome

AF:

0.696

Gnomad4 NFE exome

AF:

0.634

Gnomad4 OTH exome

AF:

0.632

GnomAD4 genome

AF:

0.687

AC:

104314

AN:

151768

Hom.:

36245

Cov.:

AF XY:

0.687

AC XY:

50975

AN XY:

74180

show subpopulations

Gnomad4 AFR

AF:

0.781

Gnomad4 AMR

AF:

0.723

Gnomad4 ASJ

AF:

0.699

Gnomad4 EAS

AF:

0.552

Gnomad4 SAS

AF:

0.498

Gnomad4 FIN

AF:

0.704

Gnomad4 NFE

AF:

0.643

Gnomad4 OTH

AF:

0.680

Alfa

AF:

0.605

Hom.:

3352

Bravo

AF:

0.696

Asia WGS

AF:

0.543

AC:

1890

AN:

3478

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over