Variant rs2302831 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.1116+35A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 1,479,704 control chromosomes in the GnomAD database, including 507 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.020 ( 47 hom., cov: 31)

Exomes 𝑓: 0.022 ( 460 hom. )

Consequence

POMT2
NM_013382.7 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.00900

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 14-77296129-T-C is Benign according to our data. Variant chr14-77296129-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 260289.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-77296129-T-C is described in Lovd as [Benign].

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0591 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.1116+35A>G		intron_variant		ENST00000261534.9	NP_037514.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POMT2	ENST00000261534.9 linkuse as main transcript	c.1116+35A>G		intron_variant		1	NM_013382.7	ENSP00000261534	P1	Q9UKY4-1

Frequencies

GnomAD3 genomes

AF:

0.0197

AC:

2997

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00463

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0342

Gnomad ASJ

AF:

0.0596

Gnomad EAS

AF:

0.0178

Gnomad SAS

AF:

0.0470

Gnomad FIN

AF:

0.0167

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0219

Gnomad OTH

AF:

0.0325

GnomAD3 exomes

AF:

0.0267

AC:

4685

AN:

175198

Hom.:

AF XY:

0.0280

AC XY:

2582

AN XY:

92374

show subpopulations

Gnomad AFR exome

AF:

0.00316

Gnomad AMR exome

AF:

0.0334

Gnomad ASJ exome

AF:

0.0557

Gnomad EAS exome

AF:

0.0128

Gnomad SAS exome

AF:

0.0446

Gnomad FIN exome

AF:

0.0174

Gnomad NFE exome

AF:

0.0224

Gnomad OTH exome

AF:

0.0358

GnomAD4 exome

AF:

0.0221

AC:

29353

AN:

1327426

Hom.:

460

Cov.:

AF XY:

0.0233

AC XY:

15371

AN XY:

660650

show subpopulations

Gnomad4 AFR exome

AF:

0.00357

Gnomad4 AMR exome

AF:

0.0332

Gnomad4 ASJ exome

AF:

0.0574

Gnomad4 EAS exome

AF:

0.0210

Gnomad4 SAS exome

AF:

0.0473

Gnomad4 FIN exome

AF:

0.0172

Gnomad4 NFE exome

AF:

0.0193

Gnomad4 OTH exome

AF:

0.0261

GnomAD4 genome

AF:

0.0196

AC:

2992

AN:

152278

Hom.:

Cov.:

AF XY:

0.0205

AC XY:

1530

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00459

Gnomad4 AMR

AF:

0.0341

Gnomad4 ASJ

AF:

0.0596

Gnomad4 EAS

AF:

0.0176

Gnomad4 SAS

AF:

0.0466

Gnomad4 FIN

AF:

0.0167

Gnomad4 NFE

AF:

0.0219

Gnomad4 OTH

AF:

0.0317

Alfa

AF:

0.0268

Hom.:

Bravo

AF:

0.0187

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 15, 2018	- -
Likely 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

-0.90

CADD

Benign

1.1

DANN

Benign

0.34

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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