3-43090952-C-T

Variant names:

• chr3-43090952-C-T
• rs488069
• NM_032806.6:c.-105-9416G>A

Variant summary

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

The NM_032806.6(POMGNT2):​c.-105-9416G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,152 control chromosomes in the GnomAD database, including 47,059 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 0.79 (47059 hom., cov: 32)
• Consequence: POMGNT2 NM_032806.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

Genes affected

POMGNT2 (HGNC:25902): (protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)) This gene encodes a protein with glycosyltransferase activity although its function is not currently known. [provided by RefSeq, Sep 2012]

LOC107986079 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POMGNT2	NM_032806.6	c.-105-9416G>A		intron_variant	Intron 1 of 1	ENST00000344697.3	NP_116195.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POMGNT2	ENST00000344697.3	c.-105-9416G>A		intron_variant	Intron 1 of 1	1	NM_032806.6	ENSP00000344125.2

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119584 AN: 152034 Hom.: 47020 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.787 AC: 119679 AN: 152152 Hom.: 47059 Cov.: 32 AF XY: 0.787 AC XY: 58544 AN XY: 74392

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.787

Alfa AF: 0.792 Hom.: 62920

Bravo AF: 0.788

Asia WGS AF: 0.735 AC: 2556 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	2.6
DANN	Benign	0.33

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: rs488069; hg19: chr3-43132444;