Variant rs71413457 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000261534.9(POMT2):c.1654-41G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 1,613,826 control chromosomes in the GnomAD database, including 407 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 31 hom., cov: 33)

Exomes 𝑓: 0.021 ( 376 hom. )

Consequence

POMT2
ENST00000261534.9 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.482

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=-0.85).

BP6

Variant 14-77280504-C-G is Benign according to our data. Variant chr14-77280504-C-G is described in ClinVar as [Benign]. Clinvar id is 260296.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-77280504-C-G is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.016 (2437/152310) while in subpopulation AMR AF= 0.0234 (358/15306). AF 95% confidence interval is 0.0223. There are 31 homozygotes in gnomad4. There are 1119 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 31 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POMT2	NM_013382.7 linkuse as main transcript	c.1654-41G>C		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.1654-41G>C		intron_variant		1	NM_013382.7	ENSP00000261534	P1	Q9UKY4-1

Frequencies

GnomAD3 genomes

AF:

0.0160

AC:

2436

AN:

152192

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00444

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0234

Gnomad ASJ

AF:

0.0470

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00600

Gnomad FIN

AF:

0.00565

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0232

Gnomad OTH

AF:

0.0234

GnomAD3 exomes

AF:

0.0167

AC:

4179

AN:

250784

Hom.:

AF XY:

0.0168

AC XY:

2278

AN XY:

135598

show subpopulations

Gnomad AFR exome

AF:

0.00431

Gnomad AMR exome

AF:

0.0149

Gnomad ASJ exome

AF:

0.0495

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00448

Gnomad FIN exome

AF:

0.00664

Gnomad NFE exome

AF:

0.0237

Gnomad OTH exome

AF:

0.0211

GnomAD4 exome

AF:

0.0207

AC:

30319

AN:

1461516

Hom.:

376

Cov.:

AF XY:

0.0203

AC XY:

14726

AN XY:

727076

show subpopulations

Gnomad4 AFR exome

AF:

0.00376

Gnomad4 AMR exome

AF:

0.0154

Gnomad4 ASJ exome

AF:

0.0506

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00478

Gnomad4 FIN exome

AF:

0.00659

Gnomad4 NFE exome

AF:

0.0235

Gnomad4 OTH exome

AF:

0.0209

GnomAD4 genome

AF:

0.0160

AC:

2437

AN:

152310

Hom.:

Cov.:

AF XY:

0.0150

AC XY:

1119

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.00443

Gnomad4 AMR

AF:

0.0234

Gnomad4 ASJ

AF:

0.0470

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00601

Gnomad4 FIN

AF:

0.00565

Gnomad4 NFE

AF:

0.0233

Gnomad4 OTH

AF:

0.0232

Alfa

AF:

0.0213

Hom.:

Bravo

AF:

0.0175

Asia WGS

AF:

0.00606

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.8

DANN

Benign

0.40

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