rs2936818

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032806.6(POMGNT2):c.-43C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,460,022 control chromosomes in the GnomAD database, including 163,239 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 14588 hom., cov: 33)

Exomes 𝑓: 0.47 ( 148651 hom. )

Consequence

POMGNT2
NM_032806.6 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.605

Publications

6 publications found

Variant links:

Genes affected

POMGNT2 (HGNC:25902): (protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)) This gene encodes a protein with glycosyltransferase activity although its function is not currently known. [provided by RefSeq, Sep 2012]

POMGNT2 Gene-Disease associations (from GenCC):

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
myopathy caused by variation in POMGNT2
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
muscular dystrophy-dystroglycanopathy, type A
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

POMGNT2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 3-43081474-G-A is Benign according to our data. Variant chr3-43081474-G-A is described in ClinVar as Benign. ClinVar VariationId is 262102.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
POMGNT2	NM_032806.6 link	c.-43C>T	5_prime_UTR_variant	Exon 2 of 2	ENST00000344697.3	NP_116195.2	Q8NAT1A0A024R2P4
POMGNT2	NM_001437285.1 link	c.-43C>T	5_prime_UTR_variant	Exon 3 of 3		NP_001424214.1
POMGNT2	XM_011534163.3 link	c.-43C>T	5_prime_UTR_variant	Exon 3 of 3		XP_011532465.1	Q8NAT1A0A024R2P4
POMGNT2	XM_017007353.2 link	c.-43C>T	5_prime_UTR_variant	Exon 4 of 4		XP_016862842.1	Q8NAT1A0A024R2P4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POMGNT2	ENST00000344697.3 link	c.-43C>T		5_prime_UTR_variant	Exon 2 of 2	1	NM_032806.6	ENSP00000344125.2		Q8NAT1

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64548

AN:

151926

Hom.:

14578

Cov.:

show subpopulations

Gnomad AFR

AF:

0.273

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.555

Gnomad ASJ

AF:

0.511

Gnomad EAS

AF:

0.623

Gnomad SAS

AF:

0.466

Gnomad FIN

AF:

0.388

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.469

Gnomad OTH

AF:

0.456

GnomAD2 exomes

AF:

0.491

AC:

50306

AN:

102478

AF XY:

0.492

show subpopulations

Gnomad AFR exome

AF:

0.265

Gnomad AMR exome

AF:

0.619

Gnomad ASJ exome

AF:

0.530

Gnomad EAS exome

AF:

0.629

Gnomad FIN exome

AF:

0.395

Gnomad NFE exome

AF:

0.480

Gnomad OTH exome

AF:

0.492

GnomAD4 exome

AF:

0.474

AC:

619935

AN:

1307978

Hom.:

148651

Cov.:

AF XY:

0.474

AC XY:

302012

AN XY:

637480

show subpopulations

African (AFR)

AF:

0.266

AC:

7702

AN:

28916

American (AMR)

AF:

0.599

AC:

14500

AN:

24190

Ashkenazi Jewish (ASJ)

AF:

0.512

AC:

9915

AN:

19366

East Asian (EAS)

AF:

0.608

AC:

21741

AN:

35738

South Asian (SAS)

AF:

0.456

AC:

30159

AN:

66092

European-Finnish (FIN)

AF:

0.390

AC:

17114

AN:

43880

Middle Eastern (MID)

AF:

0.483

AC:

2225

AN:

4604

European-Non Finnish (NFE)

AF:

0.476

AC:

490725

AN:

1031034

Other (OTH)

AF:

0.477

AC:

25854

AN:

54158

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

16624

33248

49873

66497

83121

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15196

30392

45588

60784

75980

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.425

AC:

64585

AN:

152044

Hom.:

14588

Cov.:

AF XY:

0.426

AC XY:

31692

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.273

AC:

11313

AN:

41464

American (AMR)

AF:

0.555

AC:

8489

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.511

AC:

1771

AN:

3468

East Asian (EAS)

AF:

0.623

AC:

3206

AN:

5142

South Asian (SAS)

AF:

0.465

AC:

2235

AN:

4808

European-Finnish (FIN)

AF:

0.388

AC:

4111

AN:

10598

Middle Eastern (MID)

AF:

0.527

AC:

155

AN:

294

European-Non Finnish (NFE)

AF:

0.469

AC:

31897

AN:

67970

Other (OTH)

AF:

0.453

AC:

956

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1840

3679

5519

7358

9198

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

612

1224

1836

2448

3060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.442

Hom.:

21791

Bravo

AF:

0.434

Asia WGS

AF:

0.520

AC:

1809

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jan 11, 2016

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This 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. -

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8

Benign:1

Oct 25, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 8

Benign:1

Oct 25, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.8

(source)

DANN

Benign

0.78

PhyloP100

0.60

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over