rs41292143

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_017739.4(POMGNT1):​c.1257G>A​(p.Leu419Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 1,614,166 control chromosomes in the GnomAD database, including 266 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L419L) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.010 ( 12 hom., cov: 32)
Exomes 𝑓: 0.017 ( 254 hom. )

Consequence

POMGNT1
NM_017739.4 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: -0.268
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 1-46192545-C-T is Benign according to our data. Variant chr1-46192545-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 130004.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-46192545-C-T is described in Lovd as [Benign]. Variant chr1-46192545-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-0.268 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0102 (1553/152306) while in subpopulation NFE AF= 0.0185 (1258/68024). AF 95% confidence interval is 0.0176. There are 12 homozygotes in gnomad4. There are 665 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
POMGNT1NM_017739.4 linkuse as main transcriptc.1257G>A p.Leu419Leu synonymous_variant 15/22 ENST00000371984.8 NP_060209.4 Q8WZA1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
POMGNT1ENST00000371984.8 linkuse as main transcriptc.1257G>A p.Leu419Leu synonymous_variant 15/221 NM_017739.4 ENSP00000361052.3 Q8WZA1-1

Frequencies

GnomAD3 genomes
AF:
0.0102
AC:
1552
AN:
152190
Hom.:
12
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00352
Gnomad AMI
AF:
0.00329
Gnomad AMR
AF:
0.00497
Gnomad ASJ
AF:
0.00576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.00301
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0185
Gnomad OTH
AF:
0.00526
GnomAD3 exomes
AF:
0.00889
AC:
2234
AN:
251268
Hom.:
14
AF XY:
0.00885
AC XY:
1202
AN XY:
135824
show subpopulations
Gnomad AFR exome
AF:
0.00308
Gnomad AMR exome
AF:
0.00301
Gnomad ASJ exome
AF:
0.00755
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00144
Gnomad FIN exome
AF:
0.00310
Gnomad NFE exome
AF:
0.0161
Gnomad OTH exome
AF:
0.0101
GnomAD4 exome
AF:
0.0168
AC:
24564
AN:
1461860
Hom.:
254
Cov.:
31
AF XY:
0.0162
AC XY:
11787
AN XY:
727230
show subpopulations
Gnomad4 AFR exome
AF:
0.00218
Gnomad4 AMR exome
AF:
0.00344
Gnomad4 ASJ exome
AF:
0.00685
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00205
Gnomad4 FIN exome
AF:
0.00436
Gnomad4 NFE exome
AF:
0.0207
Gnomad4 OTH exome
AF:
0.0122
GnomAD4 genome
AF:
0.0102
AC:
1553
AN:
152306
Hom.:
12
Cov.:
32
AF XY:
0.00893
AC XY:
665
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.00351
Gnomad4 AMR
AF:
0.00497
Gnomad4 ASJ
AF:
0.00576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00124
Gnomad4 FIN
AF:
0.00301
Gnomad4 NFE
AF:
0.0185
Gnomad4 OTH
AF:
0.00520
Alfa
AF:
0.0136
Hom.:
6
Bravo
AF:
0.00983
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.0164
EpiControl
AF:
0.0173

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:12
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:5
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Benign, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Likely benign, no assertion criteria providedclinical testingGenetic Services Laboratory, University of Chicago-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 providedclinical testingClinical Genetics, Academic Medical Center-- -
Benign, criteria provided, single submitterclinical testingGeneDxOct 17, 2014This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:3
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsNov 29, 2017- -
Likely benign, no assertion criteria providedclinical testingLaboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)-- -
Autosomal recessive limb-girdle muscular dystrophy type 2O Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3;C3150417:Autosomal recessive limb-girdle muscular dystrophy type 2O Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -
Muscle eye brain disease Benign:1
Benign, no assertion criteria providedclinical testingNatera, Inc.Sep 16, 2020- -
Congenital Muscular Dystrophy, alpha-dystroglycan related Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
CADD
Benign
5.8
DANN
Benign
0.67
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs41292143; hg19: chr1-46658217; API