2-134410029-G-A

Variant names:

• chr2-134410029-G-A
• rs2118844
• NM_002410.5:c.1531-2840G>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.1531-2840G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,160 control chromosomes in the GnomAD database, including 5,674 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 0.25 (5674 hom., cov: 33)
• Consequence: MGAT5 NM_002410.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAT5	NM_002410.5	c.1531-2840G>A		intron_variant	Intron 11 of 15	ENST00000281923.4	NP_002401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT5	ENST00000281923.4	c.1531-2840G>A		intron_variant	Intron 11 of 15	1	NM_002410.5	ENSP00000281923.2
MGAT5	ENST00000409645.5	c.1531-2840G>A		intron_variant	Intron 12 of 16	5		ENSP00000386377.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38610 AN: 152040 Hom.: 5662 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.254 AC: 38639 AN: 152160 Hom.: 5674 Cov.: 33 AF XY: 0.260 AC XY: 19372 AN XY: 74380

African (AFR) AF: 0.109 AC: 4546 AN: 41528

American (AMR) AF: 0.336 AC: 5132 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2005 AN: 5168

South Asian (SAS) AF: 0.467 AC: 2248 AN: 4814

European-Finnish (FIN) AF: 0.283 AC: 2998 AN: 10586

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19542 AN: 67988

Other (OTH) AF: 0.269 AC: 569 AN: 2112

Alfa AF: 0.282 Hom.: 11472

Bravo AF: 0.248

Asia WGS AF: 0.397 AC: 1383 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.21
PhyloP100		-0.12
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: rs2118844; hg19: chr2-135167600;