chr2-134206321-A-G

Variant names:

• chr2-134206321-A-G
• rs1257168
• NM_001371457.1:c.-142-47941A>G

Variant summary

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

The NM_001371457.1(MGAT5):​c.-142-47941A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,152 control chromosomes in the GnomAD database, including 34,950 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 0.66 (34950 hom., cov: 32)
• Consequence: MGAT5 NM_001371457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001371457.1. 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
	MGAT5	NM_001371457.1		c.-142-47941A>G		intron	N/A	NP_001358386.1	Q09328

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT5	ENST00000409645.5	TSL:5	c.-142-47941A>G		intron	N/A	ENSP00000386377.1	Q09328
	MGAT5	ENST00000857190.1		c.-362-43729A>G		intron	N/A	ENSP00000527249.1
	MGAT5	ENST00000857191.1		c.-143+16073A>G		intron	N/A	ENSP00000527250.1

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100363 AN: 152034 Hom.: 34873 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.661 AC: 100507 AN: 152152 Hom.: 34950 Cov.: 32 AF XY: 0.661 AC XY: 49175 AN XY: 74372

African (AFR) AF: 0.866 AC: 35971 AN: 41538

American (AMR) AF: 0.674 AC: 10315 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2572 AN: 3470

East Asian (EAS) AF: 0.835 AC: 4318 AN: 5170

South Asian (SAS) AF: 0.731 AC: 3521 AN: 4818

European-Finnish (FIN) AF: 0.495 AC: 5233 AN: 10564

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36379 AN: 67974

Other (OTH) AF: 0.692 AC: 1464 AN: 2116

Alfa AF: 0.615 Hom.: 3875

Bravo AF: 0.688

Asia WGS AF: 0.824 AC: 2863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.59
DANN	Benign	0.46
PhyloP100		-0.87
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: rs1257168; hg19: chr2-134963892;