1-46193576-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_017739.4(POMGNT1):c.1014C>T(p.Asp338Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,461,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
POMGNT1
NM_017739.4 synonymous
NM_017739.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0820
Publications
0 publications found
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]
TSPAN1 (HGNC:20657): (tetraspanin 1) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 1-46193576-G-A is Benign according to our data. Variant chr1-46193576-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 471398.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.082 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_017739.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| POMGNT1 | NM_017739.4 | MANE Select | c.1014C>T | p.Asp338Asp | synonymous | Exon 11 of 22 | NP_060209.4 | ||
| POMGNT1 | NM_001243766.2 | c.1014C>T | p.Asp338Asp | synonymous | Exon 11 of 23 | NP_001230695.2 | |||
| POMGNT1 | NM_001410783.1 | c.1014C>T | p.Asp338Asp | synonymous | Exon 11 of 22 | NP_001397712.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| POMGNT1 | ENST00000371984.8 | TSL:1 MANE Select | c.1014C>T | p.Asp338Asp | synonymous | Exon 11 of 22 | ENSP00000361052.3 | ||
| POMGNT1 | ENST00000371992.1 | TSL:2 | c.1014C>T | p.Asp338Asp | synonymous | Exon 11 of 23 | ENSP00000361060.1 | ||
| POMGNT1 | ENST00000692369.1 | c.1014C>T | p.Asp338Asp | synonymous | Exon 11 of 22 | ENSP00000508453.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.0000239 AC: 6AN: 251304 AF XY: 0.0000294 show subpopulations
GnomAD2 exomes
AF:
AC:
6
AN:
251304
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461870Hom.: 0 Cov.: 93 AF XY: 0.0000151 AC XY: 11AN XY: 727232 show subpopulations
GnomAD4 exome
AF:
AC:
19
AN:
1461870
Hom.:
Cov.:
93
AF XY:
AC XY:
11
AN XY:
727232
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
1
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
1
AN:
39700
South Asian (SAS)
AF:
AC:
3
AN:
86250
European-Finnish (FIN)
AF:
AC:
0
AN:
53408
Middle Eastern (MID)
AF:
AC:
1
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
10
AN:
1112008
Other (OTH)
AF:
AC:
3
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.472
Heterozygous variant carriers
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Allele balance
Age Distribution
Exome Het
Variant carriers
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3;C3150417:Autosomal recessive limb-girdle muscular dystrophy type 2O Benign:1
Nov 15, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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