Variant rs2292486 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_017739.4(POMGNT1):c.1111-23C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0374 in 1,614,048 control chromosomes in the GnomAD database, including 5,491 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.037 ( 473 hom., cov: 32)

Exomes 𝑓: 0.037 ( 5018 hom. )

Consequence

POMGNT1
NM_017739.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.946

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]

POMGNT1 links:

TSPAN1 (HGNC:):

TSPAN1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 1-46193238-G-A is Benign according to our data. Variant chr1-46193238-G-A is described in ClinVar as [Benign]. Clinvar id is 260870.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-46193238-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POMGNT1	NM_017739.4 linkuse as main transcript	c.1111-23C>T		intron_variant		ENST00000371984.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POMGNT1	ENST00000371984.8 linkuse as main transcript	c.1111-23C>T		intron_variant		1	NM_017739.4	P1	Q8WZA1-1

Frequencies

GnomAD3 genomes

AF:

0.0372

AC:

5658

AN:

152146

Hom.:

470

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0243

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.0344

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.344

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.0153

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0144

Gnomad OTH

AF:

0.0372

GnomAD3 exomes

AF:

0.0673

AC:

16886

AN:

251078

Hom.:

1811

AF XY:

0.0720

AC XY:

9766

AN XY:

135716

show subpopulations

Gnomad AFR exome

AF:

0.0243

Gnomad AMR exome

AF:

0.0451

Gnomad ASJ exome

AF:

0.0113

Gnomad EAS exome

AF:

0.336

Gnomad SAS exome

AF:

0.204

Gnomad FIN exome

AF:

0.0175

Gnomad NFE exome

AF:

0.0153

Gnomad OTH exome

AF:

0.0485

GnomAD4 exome

AF:

0.0375

AC:

54750

AN:

1461784

Hom.:

5018

Cov.:

AF XY:

0.0421

AC XY:

30645

AN XY:

727178

show subpopulations

Gnomad4 AFR exome

AF:

0.0255

Gnomad4 AMR exome

AF:

0.0418

Gnomad4 ASJ exome

AF:

0.0114

Gnomad4 EAS exome

AF:

0.368

Gnomad4 SAS exome

AF:

0.200

Gnomad4 FIN exome

AF:

0.0176

Gnomad4 NFE exome

AF:

0.0144

Gnomad4 OTH exome

AF:

0.0454

GnomAD4 genome

AF:

0.0372

AC:

5663

AN:

152264

Hom.:

473

Cov.:

AF XY:

0.0428

AC XY:

3188

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.0242

Gnomad4 AMR

AF:

0.0344

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.345

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.0153

Gnomad4 NFE

AF:

0.0144

Gnomad4 OTH

AF:

0.0421

Alfa

AF:

0.0199

Hom.:

Bravo

AF:

0.0355

Asia WGS

AF:

0.252

AC:

874

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 28, 2018	- -

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

- -

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.62

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over