chr7-92499847-C-CAA

Position:

• chr7-92499847-C-CAA

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS1

The NM_000466.3(PEX1):​c.2584-11_2584-10dupTT variant causes a intron change. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00039 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00029 (0 hom.)
• Consequence: PEX1 NM_000466.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 5.05

Genes affected

PEX1 (HGNC:8850): (peroxisomal biogenesis factor 1) This gene encodes a member of the AAA ATPase family, a large group of ATPases associated with diverse cellular activities. This protein is cytoplasmic but is often anchored to a peroxisomal membrane where it forms a heteromeric complex and plays a role in the import of proteins into peroxisomes and peroxisome biogenesis. Mutations in this gene have been associated with complementation group 1 peroxisomal disorders such as neonatal adrenoleukodystrophy, infantile Refsum disease, and Zellweger syndrome. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2013]

PEX1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 7-92499847-C-CAA is Benign according to our data. Variant chr7-92499847-C-CAA is described in ClinVar as [Benign]. Clinvar id is 1164265.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000294 (347/1178500) while in subpopulation AFR AF= 0.00188 (54/28650). AF 95% confidence interval is 0.00148. There are 0 homozygotes in gnomad4_exome. There are 154 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PEX1	NM_000466.3	c.2584-11_2584-10dupTT		intron_variant		ENST00000248633.9	NP_000457.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PEX1	ENST00000248633.9	c.2584-11_2584-10dupTT		intron_variant		1	NM_000466.3	ENSP00000248633.4

Frequencies

GnomAD3 genomes AF: 0.000383 AC: 56 AN: 146164 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00127

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000204

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000451

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000260 AC: 40 AN: 153898 Hom.: 0 AF XY: 0.000197 AC XY: 16 AN XY: 81294

Gnomad AFR exome AF: 0.00140

Gnomad AMR exome AF: 0.000228

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000821

Gnomad SAS exome AF: 0.000256

Gnomad FIN exome AF: 0.0000741

Gnomad NFE exome AF: 0.000158

Gnomad OTH exome AF: 0.000549

GnomAD4 exome AF: 0.000294 AC: 347 AN: 1178500 Hom.: 0 Cov.: 0 AF XY: 0.000260 AC XY: 154 AN XY: 591950

Gnomad4 AFR exome AF: 0.00188

Gnomad4 AMR exome AF: 0.000103

Gnomad4 ASJ exome AF: 0.0000446

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000110

Gnomad4 FIN exome AF: 0.000111

Gnomad4 NFE exome AF: 0.000289

Gnomad4 OTH exome AF: 0.000382

GnomAD4 genome AF: 0.000390 AC: 57 AN: 146262 Hom.: 0 Cov.: 0 AF XY: 0.000421 AC XY: 30 AN XY: 71310

Gnomad4 AFR AF: 0.00130

Gnomad4 AMR AF: 0.000203

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000452

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Zellweger spectrum disorders Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 30, 2023

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5885806; hg19: chr7-92129161;