rs972725

chr14-77281968-A-Gchr14-77281968-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013382.7(POMT2):c.1654-1505T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,114 control chromosomes in the GnomAD database, including 52,383 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (52383 hom., cov: 32)
• Consequence: POMT2 NM_013382.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POMT2	NM_013382.7	c.1654-1505T>C		intron_variant		ENST00000261534.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POMT2	ENST00000261534.9	c.1654-1505T>C		intron_variant		1	NM_013382.7	P1

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125926 AN: 151996 Hom.: 52339 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.828 AC: 126022 AN: 152114 Hom.: 52383 Cov.: 32 AF XY: 0.830 AC XY: 61686 AN XY: 74342

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.843

Alfa AF: 0.832 Hom.: 6551

Bravo AF: 0.825

Asia WGS AF: 0.885 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.58

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

Other links and lift over

dbSNP: rs972725; hg19: chr14-77748311;