dbSNP rs7153929: POMT2:c.1117-20C>T (chr14-77291400-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_013382.7(POMT2):c.1117-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 578,046 control chromosomes in the GnomAD database, including 3,351 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1264 hom., cov: 21)

Exomes 𝑓: 0.11 ( 2087 hom. )

Consequence

POMT2
NM_013382.7 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -1.21

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 14-77291400-G-A is Benign according to our data. Variant chr14-77291400-G-A is described in ClinVar as [Benign]. Clinvar id is 95533.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-77291400-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POMT2	NM_013382.7 link	c.1117-20C>T		intron_variant	Intron 9 of 20	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.1117-20C>T		intron_variant	Intron 9 of 20	1	NM_013382.7	ENSP00000261534.4		Q9UKY4-1

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

13059

AN:

115916

Hom.:

1264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.282

Gnomad AMI

AF:

0.0718

Gnomad AMR

AF:

0.0733

Gnomad ASJ

AF:

0.0605

Gnomad EAS

AF:

0.000322

Gnomad SAS

AF:

0.0687

Gnomad FIN

AF:

0.0869

Gnomad MID

AF:

0.122

Gnomad NFE

AF:

0.0411

Gnomad OTH

AF:

0.111

GnomAD3 exomes

AF:

0.0648

AC:

11401

AN:

175986

Hom.:

823

AF XY:

0.0614

AC XY:

5894

AN XY:

96020

show subpopulations

Gnomad AFR exome

AF:

0.313

Gnomad AMR exome

AF:

0.0385

Gnomad ASJ exome

AF:

0.0583

Gnomad EAS exome

AF:

0.000439

Gnomad SAS exome

AF:

0.0629

Gnomad FIN exome

AF:

0.0611

Gnomad NFE exome

AF:

0.0477

Gnomad OTH exome

AF:

0.0580

GnomAD4 exome

AF:

0.115

AC:

53027

AN:

462044

Hom.:

2087

Cov.:

AF XY:

0.109

AC XY:

26728

AN XY:

245522

show subpopulations

Gnomad4 AFR exome

AF:

0.406

Gnomad4 AMR exome

AF:

0.0484

Gnomad4 ASJ exome

AF:

0.0994

Gnomad4 EAS exome

AF:

0.000608

Gnomad4 SAS exome

AF:

0.0667

Gnomad4 FIN exome

AF:

0.0807

Gnomad4 NFE exome

AF:

0.121

Gnomad4 OTH exome

AF:

0.130

GnomAD4 genome

AF:

0.113

AC:

13078

AN:

116002

Hom.:

1264

Cov.:

AF XY:

0.115

AC XY:

6145

AN XY:

53358

show subpopulations

Gnomad4 AFR

AF:

0.282

Gnomad4 AMR

AF:

0.0732

Gnomad4 ASJ

AF:

0.0605

Gnomad4 EAS

AF:

0.000322

Gnomad4 SAS

AF:

0.0690

Gnomad4 FIN

AF:

0.0869

Gnomad4 NFE

AF:

0.0411

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.0597

Hom.:

Bravo

AF:

0.106

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

Jan 28, 2014

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. -

PreventionGenetics, part of Exact Sciences

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

- -

Jul 18, 2012

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

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

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.43

DANN

Benign

0.25

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