2-134417801-G-A

Variant names:

• chr2-134417801-G-A
• rs1530230
• NM_002410.5:c.1677+4786G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002410.5(MGAT5):​c.1677+4786G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 151,936 control chromosomes in the GnomAD database, including 1,814 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 0.13 (1814 hom., cov: 31)
• Consequence: MGAT5 NM_002410.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002410.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT5	NM_002410.5	MANE Select	c.1677+4786G>A		intron	N/A	NP_002401.1
	MGAT5	NM_001371457.1		c.1677+4786G>A		intron	N/A	NP_001358386.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT5	ENST00000281923.4	TSL:1 MANE Select	c.1677+4786G>A		intron	N/A	ENSP00000281923.2
	MGAT5	ENST00000409645.5	TSL:5	c.1677+4786G>A		intron	N/A	ENSP00000386377.1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20300 AN: 151818 Hom.: 1809 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0605

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.134 AC: 20320 AN: 151936 Hom.: 1814 Cov.: 31 AF XY: 0.134 AC XY: 9935 AN XY: 74242

African (AFR) AF: 0.231 AC: 9543 AN: 41386

American (AMR) AF: 0.127 AC: 1938 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1487 AN: 5160

South Asian (SAS) AF: 0.183 AC: 880 AN: 4802

European-Finnish (FIN) AF: 0.0605 AC: 640 AN: 10576

Middle Eastern (MID) AF: 0.231 AC: 67 AN: 290

European-Non Finnish (NFE) AF: 0.0721 AC: 4903 AN: 67966

Other (OTH) AF: 0.152 AC: 321 AN: 2110

Alfa AF: 0.0918 Hom.: 460

Bravo AF: 0.145

Asia WGS AF: 0.206 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-1.8
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: rs1530230; hg19: chr2-135175372;