3-43090952-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

POMGNT2 Gene-Disease associations (from GenCC):

• muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp, G2P
• myopathy caused by variation in POMGNT2

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• muscular dystrophy-dystroglycanopathy, type A

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

POMGNT2-AS1 (HGNC:52825):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032806.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POMGNT2	NM_032806.6	MANE Select	c.-105-9416G>A		intron	N/A	NP_116195.2
	POMGNT2	NM_001437285.1		c.-227-343G>A		intron	N/A	NP_001424214.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POMGNT2	ENST00000344697.3	TSL:1 MANE Select	c.-105-9416G>A		intron	N/A	ENSP00000344125.2	Q8NAT1
	POMGNT2	ENST00000441964.1	TSL:4	c.-227-343G>A		intron	N/A	ENSP00000408992.1	Q8NAT1
	POMGNT2	ENST00000686643.1		c.-327-343G>A		intron	N/A	ENSP00000509123.1	Q8NAT1

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

African (AFR) AF: 0.772 AC: 32054 AN: 41494

American (AMR) AF: 0.798 AC: 12217 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2660 AN: 3472

East Asian (EAS) AF: 0.718 AC: 3717 AN: 5180

South Asian (SAS) AF: 0.731 AC: 3524 AN: 4818

European-Finnish (FIN) AF: 0.820 AC: 8680 AN: 10586

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54190 AN: 67992

Other (OTH) AF: 0.787 AC: 1661 AN: 2110

Alfa AF: 0.793 Hom.: 79651

Bravo AF: 0.788

Asia WGS AF: 0.735 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.33
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs488069; hg19: chr3-43132444;