rs4954126

Variant names:

• chr2-134294500-G-A
• rs4954126
• NM_002410.5:c.407-23029G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_002410.5(MGAT5):​c.407-23029G>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
• 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=-0.96).
• 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 rank	MANE	Protein	UniProt
MGAT5	NM_002410.5	c.407-23029G>A		intron_variant	Intron 2 of 15	ENST00000281923.4	NP_002401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT5	ENST00000281923.4	c.407-23029G>A		intron_variant	Intron 2 of 15	1	NM_002410.5	ENSP00000281923.2
MGAT5	ENST00000409645.5	c.407-23029G>A		intron_variant	Intron 3 of 16	5		ENSP00000386377.1

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

African (AFR) AF: 0.849 AC: 35201 AN: 41484

American (AMR) AF: 0.893 AC: 13643 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3411 AN: 3468

East Asian (EAS) AF: 0.893 AC: 4609 AN: 5160

South Asian (SAS) AF: 0.972 AC: 4695 AN: 4828

European-Finnish (FIN) AF: 0.996 AC: 10573 AN: 10618

Middle Eastern (MID) AF: 0.942 AC: 275 AN: 292

European-Non Finnish (NFE) AF: 0.988 AC: 67202 AN: 68022

Other (OTH) AF: 0.951 AC: 2007 AN: 2110

Alfa AF: 0.971 Hom.: 266210

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
PhyloP100		-2.9
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: rs4954126; hg19: chr2-135052071;