NM_002410.5:c.2027+230A>G

Variant names:

• chr2-134442145-A-G
• rs557408
• NM_002410.5:c.2027+230A>G

Variant summary

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

The NM_002410.5(MGAT5):​c.2027+230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,118 control chromosomes in the GnomAD database, including 50,271 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 0.80 (50271 hom., cov: 31)
• Consequence: MGAT5 NM_002410.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAT5	NM_002410.5	c.2027+230A>G		intron_variant	Intron 15 of 15	ENST00000281923.4	NP_002401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT5	ENST00000281923.4	c.2027+230A>G		intron_variant	Intron 15 of 15	1	NM_002410.5	ENSP00000281923.2
MGAT5	ENST00000409645.5	c.2027+230A>G		intron_variant	Intron 16 of 16	5		ENSP00000386377.1

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121940 AN: 152000 Hom.: 50202 Cov.: 31

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.802 AC: 122068 AN: 152118 Hom.: 50271 Cov.: 31 AF XY: 0.806 AC XY: 59898 AN XY: 74346

African (AFR) AF: 0.942 AC: 39106 AN: 41518

American (AMR) AF: 0.881 AC: 13475 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3256 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5156 AN: 5162

South Asian (SAS) AF: 0.934 AC: 4514 AN: 4832

European-Finnish (FIN) AF: 0.640 AC: 6762 AN: 10568

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46986 AN: 67962

Other (OTH) AF: 0.854 AC: 1804 AN: 2112

Alfa AF: 0.754 Hom.: 5453

Bravo AF: 0.827

Asia WGS AF: 0.961 AC: 3341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.093
DANN	Benign	0.38
PhyloP100		-0.97
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: rs557408; hg19: chr2-135199716;