Submissions for variant NM_000466.3(PEX1):c.2088A>G (p.Ile696Met)

gnomAD frequency: 0.02553  dbSNP: rs35996821

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	RCV000117900	SCV000304419	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000288096	SCV000470514	benign	Peroxisome biogenesis disorder 1A (Zellweger)	2018-01-13	criteria provided, single submitter	clinical testing	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.
SIB Swiss Institute of Bioinformatics	RCV000288096	SCV000803438	benign	Peroxisome biogenesis disorder 1A (Zellweger)	2018-05-31	criteria provided, single submitter	curation	This variant is interpreted as a Benign - Stand Alone, for Peroxisome biogenesis disorder 1A (Zellweger), in Autosomal Recessive manner. The following ACMG Tag(s) were applied: BP4 => Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.). BA1 => Allele frequency is >2% in Exome Aggregation Consortium (in some populations allele frequency is >4%). BS2 => Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
Athena Diagnostics Inc	RCV000992519	SCV001144899	benign	not provided	2018-11-01	criteria provided, single submitter	clinical testing
Invitae	RCV001513794	SCV001721477	benign	Zellweger spectrum disorders	2024-02-01	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000288096	SCV001748551	benign	Peroxisome biogenesis disorder 1A (Zellweger)	2021-07-01	criteria provided, single submitter	clinical testing
GeneDx	RCV000992519	SCV001829571	likely benign	not provided	2023-10-18	criteria provided, single submitter	clinical testing	See Variant Classification Assertion Criteria.
Genetic Services Laboratory, University of Chicago	RCV000117900	SCV000152174	likely benign	not specified		no assertion criteria provided	clinical testing	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000117900	SCV001742320	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000117900	SCV001920834	benign	not specified		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000992519	SCV001928420	likely benign	not provided		no assertion criteria provided	clinical testing
Natera, Inc.	RCV001513794	SCV002076877	benign	Zellweger spectrum disorders	2017-03-29	no assertion criteria provided	clinical testing