dbSNP rs3209079: POMT2:p.Leu637Leu (chr14-77278850-A-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_013382.7(POMT2):c.1911T>G(p.Leu637Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 1,613,018 control chromosomes in the GnomAD database, including 526,421 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.82 ( 51439 hom., cov: 33)

Exomes 𝑓: 0.81 ( 474982 hom. )

Consequence

POMT2
NM_013382.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -0.748

Variant links:

Genes affected

POMT2 (HGNC:19743): (protein O-mannosyltransferase 2) The protein encoded by this gene is an O-mannosyltransferase that requires interaction with the product of the POMT1 gene for enzymatic function. The encoded protein is found in the membrane of the endoplasmic reticulum. Defects in this gene are a cause of Walker-Warburg syndrome (WWS).[provided by RefSeq, Oct 2008]

POMT2 links:

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=-0.79).

BP6

Variant 14-77278850-A-C is Benign according to our data. Variant chr14-77278850-A-C is described in ClinVar as [Benign]. Clinvar id is 166901.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-77278850-A-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.748 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POMT2	NM_013382.7 link	c.1911T>G	p.Leu637Leu	synonymous_variant	Exon 19 of 21	ENST00000261534.9	NP_037514.2	Q9UKY4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POMT2	ENST00000261534.9 link	c.1911T>G	p.Leu637Leu	synonymous_variant	Exon 19 of 21	1	NM_013382.7	ENSP00000261534.4		Q9UKY4-1

Frequencies

GnomAD3 genomes

AF:

0.821

AC:

124889

AN:

152092

Hom.:

51399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.838

Gnomad AMI

AF:

0.849

Gnomad AMR

AF:

0.761

Gnomad ASJ

AF:

0.831

Gnomad EAS

AF:

0.951

Gnomad SAS

AF:

0.785

Gnomad FIN

AF:

0.857

Gnomad MID

AF:

0.753

Gnomad NFE

AF:

0.811

Gnomad OTH

AF:

0.833

GnomAD3 exomes

AF:

0.815

AC:

203865

AN:

250248

Hom.:

83457

AF XY:

0.814

AC XY:

110302

AN XY:

135472

show subpopulations

Gnomad AFR exome

AF:

0.842

Gnomad AMR exome

AF:

0.737

Gnomad ASJ exome

AF:

0.819

Gnomad EAS exome

AF:

0.964

Gnomad SAS exome

AF:

0.775

Gnomad FIN exome

AF:

0.847

Gnomad NFE exome

AF:

0.814

Gnomad OTH exome

AF:

0.814

GnomAD4 exome

AF:

0.805

AC:

1176648

AN:

1460808

Hom.:

474982

Cov.:

AF XY:

0.805

AC XY:

584837

AN XY:

726742

show subpopulations

Gnomad4 AFR exome

AF:

0.844

Gnomad4 AMR exome

AF:

0.747

Gnomad4 ASJ exome

AF:

0.823

Gnomad4 EAS exome

AF:

0.967

Gnomad4 SAS exome

AF:

0.772

Gnomad4 FIN exome

AF:

0.845

Gnomad4 NFE exome

AF:

0.801

Gnomad4 OTH exome

AF:

0.812

GnomAD4 genome

AF:

0.821

AC:

124983

AN:

152210

Hom.:

51439

Cov.:

AF XY:

0.823

AC XY:

61244

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.838

Gnomad4 AMR

AF:

0.760

Gnomad4 ASJ

AF:

0.831

Gnomad4 EAS

AF:

0.951

Gnomad4 SAS

AF:

0.785

Gnomad4 FIN

AF:

0.857

Gnomad4 NFE

AF:

0.811

Gnomad4 OTH

AF:

0.836

Alfa

AF:

0.809

Hom.:

31665

Bravo

AF:

0.816

Asia WGS

AF:

0.874

AC:

3042

AN:

3478

EpiCase

AF:

0.809

EpiControl

AF:

0.811

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Jun 05, 2013

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Nov 24, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Leu637Leu in exon 19 of POMT2: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 19.0% (1637/8600) o f European American chromosomes from a broad population by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS; dbSNP rs3209079). -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2;C3150416:Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2;C3150418:Autosomal recessive limb-girdle muscular dystrophy type 2N

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2

Benign:1

Oct 25, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal recessive limb-girdle muscular dystrophy type 2N

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 (congenital with brain and eye anomalies), type A2

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

-0.79

CADD

Benign

5.7

DANN

Benign

0.55

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.

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