dbSNP rs2936818: POMGNT2:c.-43C>T (chr3-43081474-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 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=-0.8).

BP6

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

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	XM_005265515.4 link	c.-43C>T	5_prime_UTR_variant	Exon 3 of 3		XP_005265572.1	Q8NAT1A0A024R2P4
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

GnomAD3 exomes

AF:

0.491

AC:

50306

AN:

102478

Hom.:

12693

AF XY:

0.492

AC XY:

26168

AN XY:

53142

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 SAS exome

AF:

0.473

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

Gnomad4 AFR exome

AF:

0.266

Gnomad4 AMR exome

AF:

0.599

Gnomad4 ASJ exome

AF:

0.512

Gnomad4 EAS exome

AF:

0.608

Gnomad4 SAS exome

AF:

0.456

Gnomad4 FIN exome

AF:

0.390

Gnomad4 NFE exome

AF:

0.476

Gnomad4 OTH exome

AF:

0.477

GnomAD4 genome

AF:

0.425

AC:

64585

AN:

152044

Hom.:

14588

Cov.:

AF XY:

0.426

AC XY:

31692

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.273

Gnomad4 AMR

AF:

0.555

Gnomad4 ASJ

AF:

0.511

Gnomad4 EAS

AF:

0.623

Gnomad4 SAS

AF:

0.465

Gnomad4 FIN

AF:

0.388

Gnomad4 NFE

AF:

0.469

Gnomad4 OTH

AF:

0.453

Alfa

AF:

0.453

Hom.:

12995

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

DANN

Benign

0.78

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