rs2098380

Positions:

• chr14-77280680-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_013382.7(POMT2):​c.1654-217A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 148,644 control chromosomes in the GnomAD database, including 9,665 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.33 (9665 hom., cov: 33)
• Consequence: POMT2 NM_013382.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.81

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 14-77280680-T-C is Benign according to our data. Variant chr14-77280680-T-C is described in ClinVar as [Benign]. Clinvar id is 668037.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POMT2	NM_013382.7	c.1654-217A>G		intron_variant		ENST00000261534.9	NP_037514.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POMT2	ENST00000261534.9	c.1654-217A>G		intron_variant		1	NM_013382.7	ENSP00000261534.4

Frequencies

GnomAD3 genomes AF: 0.334 AC: 49535 AN: 148528 Hom.: 9654 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.343

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.333 AC: 49559 AN: 148644 Hom.: 9665 Cov.: 33 AF XY: 0.338 AC XY: 24486 AN XY: 72476

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.350

Alfa AF: 0.386 Hom.: 15288

Bravo AF: 0.317

Asia WGS AF: 0.345 AC: 1196 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	-0.91
CADD	Benign	0.19
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs2098380; hg19: chr14-77747023;