2-134301309-C-T

Position:

• chr2-134301309-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002410.5(MGAT5):​c.407-16220C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,114 control chromosomes in the GnomAD database, including 3,433 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 0.17 (3433 hom., cov: 32)
• Consequence: MGAT5 NM_002410.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAT5	NM_002410.5	c.407-16220C>T		intron_variant		ENST00000281923.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT5	ENST00000281923.4	c.407-16220C>T		intron_variant		1	NM_002410.5	P1
MGAT5	ENST00000409645.5	c.407-16220C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26570 AN: 151996 Hom.: 3432 Cov.: 32

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0612

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.175 AC: 26559 AN: 152114 Hom.: 3433 Cov.: 32 AF XY: 0.174 AC XY: 12910 AN XY: 74358

Gnomad4 AFR AF: 0.0507

Gnomad4 AMR AF: 0.0992

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.133

Alfa AF: 0.207 Hom.: 489

Bravo AF: 0.148

Asia WGS AF: 0.0340 AC: 117 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.38

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

Publications

LitVar

Other links and lift over

dbSNP: rs10210993; hg19: chr2-135058880;