NM_002410.5:c.407-17676A>G

Variant names:

• chr2-134299853-A-G
• rs11887041
• NM_002410.5:c.407-17676A>G

Variant summary

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

The NM_002410.5(MGAT5):​c.407-17676A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.916 in 152,194 control chromosomes in the GnomAD database, including 64,848 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 0.92 (64848 hom., cov: 32)
• Consequence: MGAT5 NM_002410.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 4 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 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.407-17676A>G		intron	N/A	NP_002401.1
	MGAT5	NM_001371457.1		c.407-17676A>G		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.407-17676A>G		intron	N/A	ENSP00000281923.2
	MGAT5	ENST00000409645.5	TSL:5	c.407-17676A>G		intron	N/A	ENSP00000386377.1

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139349 AN: 152076 Hom.: 64816 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.995

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.916 AC: 139435 AN: 152194 Hom.: 64848 Cov.: 32 AF XY: 0.919 AC XY: 68354 AN XY: 74410

African (AFR) AF: 0.735 AC: 30474 AN: 41472

American (AMR) AF: 0.957 AC: 14620 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3414 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5168 AN: 5176

South Asian (SAS) AF: 0.995 AC: 4800 AN: 4822

European-Finnish (FIN) AF: 0.995 AC: 10578 AN: 10626

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67213 AN: 68028

Other (OTH) AF: 0.934 AC: 1975 AN: 2114

Alfa AF: 0.963 Hom.: 87678

Bravo AF: 0.903

Asia WGS AF: 0.981 AC: 3408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.1
DANN	Benign	0.84
PhyloP100		0.60
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: rs11887041; hg19: chr2-135057424;