Variant rs2070925 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_002406.4(MGAT1):c.1152G>T(p.Val384Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0545 in 1,614,172 control chromosomes in the GnomAD database, including 3,315 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 0.075 ( 550 hom., cov: 33)

Exomes 𝑓: 0.052 ( 2765 hom. )

Consequence

MGAT1
NM_002406.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.350

Variant links:

Genes affected

MGAT1 (HGNC:7044): (alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase) There are believed to be over 100 different glycosyltransferases involved in the synthesis of protein-bound and lipid-bound oligosaccharides. UDP-N-acetylglucosamine:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I is a medial-Golgi enzyme essential for the synthesis of hybrid and complex N-glycans. The protein, encoded by a single exon, shows typical features of a type II transmembrane protein. The protein is believed to be essential for normal embryogenesis. Several variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

MGAT1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP7

Synonymous conserved (PhyloP=0.35 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAT1	NM_002406.4 linkuse as main transcript	c.1152G>T	p.Val384Val	synonymous_variant	2/2	ENST00000307826.5	NP_002397.2	P26572

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT1	ENST00000307826.5 linkuse as main transcript	c.1152G>T	p.Val384Val	synonymous_variant	2/2	1	NM_002406.4	ENSP00000311888.4		P26572

Frequencies

GnomAD3 genomes

AF:

0.0754

AC:

11468

AN:

152178

Hom.:

548

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.0976

Gnomad AMR

AF:

0.0485

Gnomad ASJ

AF:

0.0300

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.0911

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0434

Gnomad OTH

AF:

0.0713

GnomAD3 exomes

AF:

0.0715

AC:

17966

AN:

251354

Hom.:

1009

AF XY:

0.0724

AC XY:

9834

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.117

Gnomad AMR exome

AF:

0.0453

Gnomad ASJ exome

AF:

0.0339

Gnomad EAS exome

AF:

0.209

Gnomad SAS exome

AF:

0.110

Gnomad FIN exome

AF:

0.0821

Gnomad NFE exome

AF:

0.0426

Gnomad OTH exome

AF:

0.0554

GnomAD4 exome

AF:

0.0523

AC:

76444

AN:

1461878

Hom.:

2765

Cov.:

AF XY:

0.0538

AC XY:

39128

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.118

Gnomad4 AMR exome

AF:

0.0469

Gnomad4 ASJ exome

AF:

0.0353

Gnomad4 EAS exome

AF:

0.165

Gnomad4 SAS exome

AF:

0.107

Gnomad4 FIN exome

AF:

0.0801

Gnomad4 NFE exome

AF:

0.0409

Gnomad4 OTH exome

AF:

0.0578

GnomAD4 genome

AF:

0.0754

AC:

11482

AN:

152294

Hom.:

550

Cov.:

AF XY:

0.0793

AC XY:

5905

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.118

Gnomad4 AMR

AF:

0.0487

Gnomad4 ASJ

AF:

0.0300

Gnomad4 EAS

AF:

0.187

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.0911

Gnomad4 NFE

AF:

0.0435

Gnomad4 OTH

AF:

0.0734

Alfa

AF:

0.0471

Hom.:

Bravo

AF:

0.0752

Asia WGS

AF:

0.136

AC:

473

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

7.2

DANN

Benign

0.84

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over