Variant 14-77306486-A-G 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_013382.7(POMT2):c.334-45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,602,448 control chromosomes in the GnomAD database, including 11,093 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.087 ( 735 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10358 hom. )

Consequence

POMT2
NM_013382.7 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.561

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:

POMT2 (HGNC:):

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=-0.71).

BP6

Variant 14-77306486-A-G is Benign according to our data. Variant chr14-77306486-A-G is described in ClinVar as [Benign]. Clinvar id is 260300.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-77306486-A-G is described in Lovd as [Likely_benign]. Variant chr14-77306486-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POMT2	NM_013382.7 linkuse as main transcript	c.334-45T>C		intron_variant		ENST00000261534.9	NP_037514.2	Q9UKY4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POMT2	ENST00000261534.9 linkuse as main transcript	c.334-45T>C		intron_variant		1	NM_013382.7	ENSP00000261534.4		Q9UKY4-1

Frequencies

GnomAD3 genomes

AF:

0.0875

AC:

13310

AN:

152158

Hom.:

735

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0334

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.0661

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.00848

Gnomad SAS

AF:

0.188

Gnomad FIN

AF:

0.0955

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.0865

GnomAD3 exomes

AF:

0.104

AC:

25729

AN:

246266

Hom.:

1708

AF XY:

0.113

AC XY:

15024

AN XY:

133314

show subpopulations

Gnomad AFR exome

AF:

0.0304

Gnomad AMR exome

AF:

0.0471

Gnomad ASJ exome

AF:

0.129

Gnomad EAS exome

AF:

0.00539

Gnomad SAS exome

AF:

0.194

Gnomad FIN exome

AF:

0.101

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.113

AC:

164574

AN:

1450172

Hom.:

10358

Cov.:

AF XY:

0.117

AC XY:

84298

AN XY:

721308

show subpopulations

Gnomad4 AFR exome

AF:

0.0274

Gnomad4 AMR exome

AF:

0.0489

Gnomad4 ASJ exome

AF:

0.131

Gnomad4 EAS exome

AF:

0.00466

Gnomad4 SAS exome

AF:

0.192

Gnomad4 FIN exome

AF:

0.0988

Gnomad4 NFE exome

AF:

0.117

Gnomad4 OTH exome

AF:

0.113

GnomAD4 genome

AF:

0.0874

AC:

13312

AN:

152276

Hom.:

735

Cov.:

AF XY:

0.0886

AC XY:

6593

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.0334

Gnomad4 AMR

AF:

0.0658

Gnomad4 ASJ

AF:

0.124

Gnomad4 EAS

AF:

0.00850

Gnomad4 SAS

AF:

0.189

Gnomad4 FIN

AF:

0.0955

Gnomad4 NFE

AF:

0.120

Gnomad4 OTH

AF:

0.0856

Alfa

AF:

0.105

Hom.:

215

Bravo

AF:

0.0784

Asia WGS

AF:

0.117

AC:

411

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	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. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.86

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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