rs1257169

chr2-134206291-C-Achr2-134206291-C-Gchr2-134206291-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• 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/exons	MANE	UniProt
MGAT5	NM_001371457.1	c.-142-47971C>A		intron_variant
MGAT5	XM_005263669.6	c.-139-47974C>A		intron_variant
MGAT5	XM_006712534.4	c.-360+16043C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT5	ENST00000409645.5	c.-142-47971C>A		intron_variant		5		P1
MGAT5	ENST00000468758.1	n.310-46804C>A		intron_variant, non_coding_transcript_variant		5
MGAT5	ENST00000481801.5	n.310-47974C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.690

Alfa AF: 0.609 Hom.: 11124

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

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: rs1257169; hg19: chr2-134963862;