Variant 14-77283714-T-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.1653+83A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 1,177,070 control chromosomes in the GnomAD database, including 168,817 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 21034 hom., cov: 32)

Exomes 𝑓: 0.53 ( 147783 hom. )

Consequence

POMT2
NM_013382.7 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.77

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=-0.81).

BP6

Variant 14-77283714-T-G is Benign according to our data. Variant chr14-77283714-T-G is described in ClinVar as [Benign]. Clinvar id is 670967.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 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.1653+83A>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.1653+83A>C		intron_variant		1	NM_013382.7	ENSP00000261534.4		Q9UKY4-1

Frequencies

GnomAD3 genomes

AF:

0.523

AC:

79393

AN:

151806

Hom.:

21016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.485

Gnomad AMI

AF:

0.572

Gnomad AMR

AF:

0.454

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.473

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.617

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.556

Gnomad OTH

AF:

0.510

GnomAD4 exome

AF:

0.534

AC:

546951

AN:

1025146

Hom.:

147783

AF XY:

0.532

AC XY:

281651

AN XY:

529048

show subpopulations

Gnomad4 AFR exome

AF:

0.482

Gnomad4 AMR exome

AF:

0.387

Gnomad4 ASJ exome

AF:

0.485

Gnomad4 EAS exome

AF:

0.486

Gnomad4 SAS exome

AF:

0.466

Gnomad4 FIN exome

AF:

0.609

Gnomad4 NFE exome

AF:

0.552

Gnomad4 OTH exome

AF:

0.518

GnomAD4 genome

AF:

0.523

AC:

79447

AN:

151924

Hom.:

21034

Cov.:

AF XY:

0.523

AC XY:

38834

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.485

Gnomad4 AMR

AF:

0.453

Gnomad4 ASJ

AF:

0.484

Gnomad4 EAS

AF:

0.475

Gnomad4 SAS

AF:

0.474

Gnomad4 FIN

AF:

0.617

Gnomad4 NFE

AF:

0.556

Gnomad4 OTH

AF:

0.515

Alfa

AF:

0.541

Hom.:

34665

Bravo

AF:

0.506

Asia WGS

AF:

0.494

AC:

1716

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.082

DANN

Benign

0.34

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