rs4954126

Positions:

• chr2-134294500-G-A
• chr2-134294500-G-T

Variant summary

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

The NM_002410.5(MGAT5):​c.407-23029G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.937 in 152,180 control chromosomes in the GnomAD database, including 67,108 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 0.94 (67108 hom., cov: 31)
• Consequence: MGAT5 NM_002410.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAT5	NM_002410.5	c.407-23029G>A		intron_variant		ENST00000281923.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT5	ENST00000281923.4	c.407-23029G>A		intron_variant		1	NM_002410.5	P1
MGAT5	ENST00000409645.5	c.407-23029G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142423 AN: 152062 Hom.: 67061 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.937 AC: 142528 AN: 152180 Hom.: 67108 Cov.: 31 AF XY: 0.935 AC XY: 69568 AN XY: 74400

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.972

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.951

Alfa AF: 0.978 Hom.: 113020

Bravo AF: 0.926

Asia WGS AF: 0.922 AC: 3204 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0050
DANN	Benign	0.19

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: rs4954126; hg19: chr2-135052071;