dbSNP rs79509556: POMT2:c.1007-32G>A (chr14-77296305-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_013382.7(POMT2):c.1007-32G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0291 in 1,483,100 control chromosomes in the GnomAD database, including 806 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 ( 37 hom., cov: 31)

Exomes 𝑓: 0.030 ( 769 hom. )

Consequence

POMT2
NM_013382.7 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.0170

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=-0.8).

BP6

Variant 14-77296305-C-T is Benign according to our data. Variant chr14-77296305-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 260288.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-77296305-C-T is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.02 (3038/152264) while in subpopulation NFE AF= 0.0319 (2171/68016). AF 95% confidence interval is 0.0308. There are 37 homozygotes in gnomad4. There are 1411 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 37 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POMT2	NM_013382.7 link	c.1007-32G>A		intron_variant	Intron 8 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.1007-32G>A		intron_variant	Intron 8 of 20	1	NM_013382.7	ENSP00000261534.4		Q9UKY4-1

Frequencies

GnomAD3 genomes

AF:

0.0200

AC:

3040

AN:

152146

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00499

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.0156

Gnomad ASJ

AF:

0.0222

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.00538

Gnomad FIN

AF:

0.0220

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0319

Gnomad OTH

AF:

0.0229

GnomAD3 exomes

AF:

0.0200

AC:

3525

AN:

175870

Hom.:

AF XY:

0.0202

AC XY:

1877

AN XY:

93138

show subpopulations

Gnomad AFR exome

AF:

0.00528

Gnomad AMR exome

AF:

0.0124

Gnomad ASJ exome

AF:

0.0201

Gnomad EAS exome

AF:

0.0000751

Gnomad SAS exome

AF:

0.00660

Gnomad FIN exome

AF:

0.0206

Gnomad NFE exome

AF:

0.0324

Gnomad OTH exome

AF:

0.0261

GnomAD4 exome

AF:

0.0302

AC:

40165

AN:

1330836

Hom.:

769

Cov.:

AF XY:

0.0294

AC XY:

19510

AN XY:

662784

show subpopulations

Gnomad4 AFR exome

AF:

0.00453

Gnomad4 AMR exome

AF:

0.0134

Gnomad4 ASJ exome

AF:

0.0216

Gnomad4 EAS exome

AF:

0.0000537

Gnomad4 SAS exome

AF:

0.00656

Gnomad4 FIN exome

AF:

0.0205

Gnomad4 NFE exome

AF:

0.0355

Gnomad4 OTH exome

AF:

0.0281

GnomAD4 genome

AF:

0.0200

AC:

3038

AN:

152264

Hom.:

Cov.:

AF XY:

0.0190

AC XY:

1411

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00498

Gnomad4 AMR

AF:

0.0156

Gnomad4 ASJ

AF:

0.0222

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00539

Gnomad4 FIN

AF:

0.0220

Gnomad4 NFE

AF:

0.0319

Gnomad4 OTH

AF:

0.0227

Alfa

AF:

0.0268

Hom.:

Bravo

AF:

0.0193

Asia WGS

AF:

0.00318

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 29, 2016

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 14, 2018

GeneDx

Significance: Likely 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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.6

DANN

Benign

0.85

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