2-134347807-A-G

Position:

• chr2-134347807-A-G

Variant summary

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

The NM_002410.5(MGAT5):​c.1113-1998A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,040 control chromosomes in the GnomAD database, including 25,777 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 0.55 (25777 hom., cov: 32)
• Consequence: MGAT5 NM_002410.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

MGAT5 (HGNC:7049): (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase) The protein encoded by this gene belongs to the glycosyltransferase family. It catalyzes the addition of beta-1,6-N-acetylglucosamine to the alpha-linked mannose of biantennary N-linked oligosaccharides present on the newly synthesized glycoproteins. It is one of the most important enzymes involved in the regulation of the biosynthesis of glycoprotein oligosaccharides. Alterations of the oligosaccharides on cell surface glycoproteins cause significant changes in the adhesive or migratory behavior of a cell. Increase in the activity of this enzyme has been correlated with the progression of invasive malignancies. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAT5	NM_002410.5	c.1113-1998A>G		intron_variant		ENST00000281923.4	NP_002401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT5	ENST00000281923.4	c.1113-1998A>G		intron_variant		1	NM_002410.5	ENSP00000281923	P1
MGAT5	ENST00000409645.5	c.1113-1998A>G		intron_variant		5		ENSP00000386377	P1

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83933 AN: 151922 Hom.: 25767 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.552 AC: 83957 AN: 152040 Hom.: 25777 Cov.: 32 AF XY: 0.556 AC XY: 41321 AN XY: 74304

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.558

Alfa AF: 0.626 Hom.: 33510

Bravo AF: 0.537

Asia WGS AF: 0.608 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.62

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: rs6707591; hg19: chr2-135105378;