rs7160195

chr14-77320032-G-Achr14-77320032-G-C

Variant summary

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

The NM_013382.7(POMT2):c.248+402C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,014 control chromosomes in the GnomAD database, including 8,306 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 0.33 (8306 hom., cov: 32)
• Consequence: POMT2 NM_013382.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POMT2	NM_013382.7	c.248+402C>T		intron_variant		ENST00000261534.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POMT2	ENST00000261534.9	c.248+402C>T		intron_variant		1	NM_013382.7	P1

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49678 AN: 151896 Hom.: 8288 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.327 AC: 49721 AN: 152014 Hom.: 8306 Cov.: 32 AF XY: 0.325 AC XY: 24165 AN XY: 74294

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.307

Alfa AF: 0.342 Hom.: 1297

Bravo AF: 0.321

Asia WGS AF: 0.295 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.8
Dann	Benign	0.54

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: rs7160195; hg19: chr14-77786375;