2-134216210-G-C

Variant names:

• chr2-134216210-G-C
• rs10496722
• NM_001371457.1:c.-142-38052G>C

Variant summary

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

The NM_001371457.1(MGAT5):​c.-142-38052G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0437 in 152,160 control chromosomes in the GnomAD database, including 356 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 0.044 (356 hom., cov: 32)
• Consequence: MGAT5 NM_001371457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAT5	NM_001371457.1	c.-142-38052G>C		intron_variant	Intron 1 of 16		NP_001358386.1
MGAT5	XM_005263669.6	c.-139-38055G>C		intron_variant	Intron 1 of 16		XP_005263726.1
MGAT5	XM_006712534.4	c.-360+25962G>C		intron_variant	Intron 3 of 20		XP_006712597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT5	ENST00000409645.5	c.-142-38052G>C		intron_variant	Intron 1 of 16	5		ENSP00000386377.1
MGAT5	ENST00000468758.1	n.310-36885G>C		intron_variant	Intron 1 of 2	5
MGAT5	ENST00000481801.5	n.310-38055G>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0437 AC: 6645 AN: 152042 Hom.: 355 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.00950

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.0380

Gnomad FIN AF: 0.000660

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00587

Gnomad OTH AF: 0.0307

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

GnomAD4 genome AF: 0.0437 AC: 6652 AN: 152160 Hom.: 356 Cov.: 32 AF XY: 0.0424 AC XY: 3153 AN XY: 74398

African (AFR) AF: 0.112 AC: 4667 AN: 41492

American (AMR) AF: 0.0618 AC: 943 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00950 AC: 33 AN: 3472

East Asian (EAS) AF: 0.0675 AC: 350 AN: 5186

South Asian (SAS) AF: 0.0378 AC: 182 AN: 4818

European-Finnish (FIN) AF: 0.000660 AC: 7 AN: 10604

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00587 AC: 399 AN: 68016

Other (OTH) AF: 0.0303 AC: 64 AN: 2110

Alfa AF: 0.00201 Hom.: 1

Bravo AF: 0.0534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.52
DANN	Benign	0.48
PhyloP100		-0.99
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: rs10496722; hg19: chr2-134973781;