Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_017739.4(POMGNT1):āc.681A>Gā(p.Lys227=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 1,613,968 control chromosomes in the GnomAD database, including 103,172 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. K227?) has been classified as Likely pathogenic.
POMGNT1 (HGNC:19139): (protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)) This gene encodes a type II transmembrane protein that resides in the Golgi apparatus. It participates in O-mannosyl glycosylation and is specific for alpha linked terminal mannose. Mutations in this gene may be associated with muscle-eye-brain disease and several congenital muscular dystrophies. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]
BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (MetaRNN=0.0029520392).
BP6
?
BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-46194623-T-C is Benign according to our data. Variant chr1-46194623-T-C is described in ClinVar as [Benign]. Clinvar id is 95761.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-46194623-T-C is described in Lovd as [Benign].
BP7
?
BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.397 with no splicing effect.
BA1
?
BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Nov 26, 2014
p.Lys227Lys in exon 8 of POMGNT1: This variant is not expected to have clinical significance because it has been identified in 35% (3000/8600) of European Ameri can chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington. edu/EVS/; dbSNP rs2292487). -
Likely benign, no assertion criteria provided
clinical testing
Genetic Services Laboratory, University of Chicago
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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. -
Benign, no assertion criteria provided
clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
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Benign, no assertion criteria provided
clinical testing
Clinical Genetics, Academic Medical Center
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Benign, no assertion criteria provided
clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
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Autosomal recessive limb-girdle muscular dystrophy type 2O Benign:2
Benign, criteria provided, single submitter
clinical testing
Genome-Nilou Lab
Oct 25, 2021
- -
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. -
not provided Benign:2
Benign, criteria provided, single submitter
clinical testing
GeneDx
Mar 03, 2015
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Benign, criteria provided, single submitter
clinical testing
Athena Diagnostics
Apr 14, 2017
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Retinitis pigmentosa 76 Benign:1
Benign, criteria provided, single submitter
clinical testing
Genome-Nilou Lab
Jul 01, 2021
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Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3;C3150417:Autosomal recessive limb-girdle muscular dystrophy type 2O Benign:1
Benign, criteria provided, single submitter
clinical testing
Invitae
Feb 01, 2024
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Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 Benign:1
Benign, criteria provided, single submitter
clinical testing
Genome-Nilou Lab
Oct 25, 2021
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Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3 Benign:1
Benign, criteria provided, single submitter
clinical testing
Genome-Nilou Lab
Jul 01, 2021
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Retinal dystrophy Benign:1
Benign, criteria provided, single submitter
research
Dept Of Ophthalmology, Nagoya University
Oct 01, 2023
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Muscle eye brain disease Benign:1
Benign, no assertion criteria provided
clinical testing
Natera, Inc.
Sep 16, 2020
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Congenital Muscular Dystrophy, alpha-dystroglycan related 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. -