rs41309197
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_017739.4(POMGNT1):c.235+33T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0242 in 1,614,094 control chromosomes in the GnomAD database, including 808 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.041 ( 203 hom., cov: 33)
Exomes 𝑓: 0.022 ( 605 hom. )
Consequence
POMGNT1
NM_017739.4 intron
NM_017739.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.318
Genes affected
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 1-46196937-A-C is Benign according to our data. Variant chr1-46196937-A-C is described in ClinVar as [Benign]. Clinvar id is 260873.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-46196937-A-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0831 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMGNT1 | NM_017739.4 | c.235+33T>G | intron_variant | ENST00000371984.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMGNT1 | ENST00000371984.8 | c.235+33T>G | intron_variant | 1 | NM_017739.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0409 AC: 6228AN: 152108Hom.: 203 Cov.: 33
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GnomAD3 exomes AF: 0.0291 AC: 7319AN: 251488Hom.: 181 AF XY: 0.0292 AC XY: 3965AN XY: 135918
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GnomAD4 exome AF: 0.0225 AC: 32831AN: 1461868Hom.: 605 Cov.: 33 AF XY: 0.0231 AC XY: 16763AN XY: 727242
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GnomAD4 genome ? AF: 0.0409 AC: 6232AN: 152226Hom.: 203 Cov.: 33 AF XY: 0.0422 AC XY: 3143AN XY: 74436
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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 | - | - - |
Retinitis pigmentosa 76 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 2018 | - - |
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 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at