rs4899650

chr14-77310158-T-Achr14-77310158-T-Cchr14-77310158-T-G

Variant summary

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

The NM_013382.7(POMT2):c.333+1791A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,064 control chromosomes in the GnomAD database, including 11,171 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 0.38 (11171 hom., cov: 32)
• Consequence: POMT2 NM_013382.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POMT2	NM_013382.7	c.333+1791A>T		intron_variant		ENST00000261534.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POMT2	ENST00000261534.9	c.333+1791A>T		intron_variant		1	NM_013382.7	P1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57812 AN: 151946 Hom.: 11146 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.381 AC: 57866 AN: 152064 Hom.: 11171 Cov.: 32 AF XY: 0.379 AC XY: 28174 AN XY: 74346

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.370

Alfa AF: 0.286 Hom.: 763

Bravo AF: 0.371

Asia WGS AF: 0.368 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.077
Dann	Benign	0.43

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: rs4899650; hg19: chr14-77776501;