NM_001371457.1:c.-142-47971C>A

Variant names:

• chr2-134206291-C-A
• rs1257169
• NM_001371457.1:c.-142-47971C>A

Variant summary

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

The NM_001371457.1(MGAT5):​c.-142-47971C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,084 control chromosomes in the GnomAD database, including 34,809 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 0.66 (34809 hom., cov: 32)
• Consequence: MGAT5 NM_001371457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAT5	NM_001371457.1	c.-142-47971C>A		intron_variant	Intron 1 of 16		NP_001358386.1
MGAT5	XM_005263669.6	c.-139-47974C>A		intron_variant	Intron 1 of 16		XP_005263726.1
MGAT5	XM_006712534.4	c.-360+16043C>A		intron_variant	Intron 3 of 20		XP_006712597.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT5	ENST00000409645.5	c.-142-47971C>A		intron_variant	Intron 1 of 16	5		ENSP00000386377.1
MGAT5	ENST00000468758.1	n.310-46804C>A		intron_variant	Intron 1 of 2	5
MGAT5	ENST00000481801.5	n.310-47974C>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100096 AN: 151966 Hom.: 34732 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.659 AC: 100240 AN: 152084 Hom.: 34809 Cov.: 32 AF XY: 0.660 AC XY: 49054 AN XY: 74348

African (AFR) AF: 0.866 AC: 35942 AN: 41516

American (AMR) AF: 0.674 AC: 10302 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2567 AN: 3468

East Asian (EAS) AF: 0.835 AC: 4309 AN: 5158

South Asian (SAS) AF: 0.730 AC: 3520 AN: 4822

European-Finnish (FIN) AF: 0.494 AC: 5217 AN: 10562

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36189 AN: 67952

Other (OTH) AF: 0.690 AC: 1461 AN: 2116

Alfa AF: 0.609 Hom.: 17506

Bravo AF: 0.687

Asia WGS AF: 0.824 AC: 2862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.25
DANN	Benign	0.48
PhyloP100		-0.41
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: rs1257169; hg19: chr2-134963862;