Genetic Variant MGAT1:p.Leu381Leu (chr5-180791831-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

17 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MGAT1	NM_002406.4 link	c.1141C>T	p.Leu381Leu	synonymous_variant	Exon 2 of 2	ENST00000307826.5	NP_002397.2	P26572

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT1	ENST00000307826.5 link	c.1141C>T	p.Leu381Leu	synonymous_variant	Exon 2 of 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

GnomAD2 exomes

AF:

0.0703

AC:

17668

AN:

251352

AF XY:

0.0718

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 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

African (AFR)

AF:

0.0908

AC:

3039

AN:

33480

American (AMR)

AF:

0.0443

AC:

1982

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0353

AC:

922

AN:

26136

East Asian (EAS)

AF:

0.193

AC:

7666

AN:

39700

South Asian (SAS)

AF:

0.107

AC:

9267

AN:

86258

European-Finnish (FIN)

AF:

0.0807

AC:

4309

AN:

53412

Middle Eastern (MID)

AF:

0.0756

AC:

436

AN:

5768

European-Non Finnish (NFE)

AF:

0.0405

AC:

44984

AN:

1112002

Other (OTH)

AF:

0.0560

AC:

3382

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

4663

9326

13990

18653

23316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1860

3720

5580

7440

9300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0675

AC:

10279

AN:

152248

Hom.:

436

Cov.:

AF XY:

0.0717

AC XY:

5337

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0897

AC:

3725

AN:

41530

American (AMR)

AF:

0.0439

AC:

672

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0300

AC:

104

AN:

3472

East Asian (EAS)

AF:

0.200

AC:

1034

AN:

5166

South Asian (SAS)

AF:

0.120

AC:

579

AN:

4818

European-Finnish (FIN)

AF:

0.0917

AC:

974

AN:

10620

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0433

AC:

2942

AN:

68018

Other (OTH)

AF:

0.0658

AC:

139

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

467

934

1401

1868

2335

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0481

Hom.:

454

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

(source)

DANN

Benign

0.85

PhyloP100

1.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over