Variant rs2070924 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002406.4(MGAT1):c.1141C>T(p.Leu381Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0534 in 1,614,124 control chromosomes in the GnomAD database, including 3,249 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 0.068 ( 436 hom., cov: 33)

Exomes 𝑓: 0.052 ( 2813 hom. )

Consequence

MGAT1
NM_002406.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.39

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP7

Synonymous conserved (PhyloP=1.39 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.19 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.1141C>T	p.Leu381Leu	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.1141C>T	p.Leu381Leu	synonymous_variant	2/2	1	NM_002406.4	ENSP00000311888.4		P26572

Frequencies

GnomAD3 genomes

AF:

0.0675

AC:

10265

AN:

152130

Hom.:

434

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0897

Gnomad AMI

AF:

0.0976

Gnomad AMR

AF:

0.0438

Gnomad ASJ

AF:

0.0300

Gnomad EAS

AF:

0.200

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0917

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0432

Gnomad OTH

AF:

0.0636

GnomAD3 exomes

AF:

0.0703

AC:

17668

AN:

251352

Hom.:

1008

AF XY:

0.0718

AC XY:

9753

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.0894

Gnomad AMR exome

AF:

0.0431

Gnomad ASJ exome

AF:

0.0339

Gnomad EAS exome

AF:

0.222

Gnomad SAS exome

AF:

0.110

Gnomad FIN exome

AF:

0.0825

Gnomad NFE exome

AF:

0.0423

Gnomad OTH exome

AF:

0.0550

GnomAD4 exome

AF:

0.0520

AC:

75987

AN:

1461876

Hom.:

2813

Cov.:

AF XY:

0.0536

AC XY:

39006

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.0908

Gnomad4 AMR exome

AF:

0.0443

Gnomad4 ASJ exome

AF:

0.0353

Gnomad4 EAS exome

AF:

0.193

Gnomad4 SAS exome

AF:

0.107

Gnomad4 FIN exome

AF:

0.0807

Gnomad4 NFE exome

AF:

0.0405

Gnomad4 OTH exome

AF:

0.0560

GnomAD4 genome

AF:

0.0675

AC:

10279

AN:

152248

Hom.:

436

Cov.:

AF XY:

0.0717

AC XY:

5337

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0897

Gnomad4 AMR

AF:

0.0439

Gnomad4 ASJ

AF:

0.0300

Gnomad4 EAS

AF:

0.200

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.0917

Gnomad4 NFE

AF:

0.0433

Gnomad4 OTH

AF:

0.0658

Alfa

AF:

0.0469

Hom.:

347

Bravo

AF:

0.0660

Asia WGS

AF:

0.142

AC:

494

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.8

DANN

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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