Variant chr22-39488352-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_002409.5(MGAT3):c.1005C>G(p.Gly335=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00808 in 1,612,586 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0053 ( 6 hom., cov: 33)

Exomes 𝑓: 0.0084 ( 60 hom. )

Consequence

MGAT3
NM_002409.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.71

Variant links:

Genes affected

MGAT3 (HGNC:7046): (beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase) There are believed to be over 100 different glycosyltransferases involved in the synthesis of protein-bound and lipid-bound oligosaccharides. The enzyme encoded by this gene transfers a GlcNAc residue to the beta-linked mannose of the trimannosyl core of N-linked oligosaccharides and produces a bisecting GlcNAc. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

MGAT3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant 22-39488352-C-G is Benign according to our data. Variant chr22-39488352-C-G is described in ClinVar as [Benign]. Clinvar id is 781620.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 813 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAT3	NM_002409.5 linkuse as main transcript	c.1005C>G	p.Gly335=	synonymous_variant	2/2	ENST00000341184.7
MGAT3	NM_001098270.2 linkuse as main transcript	c.1005C>G	p.Gly335=	synonymous_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT3	ENST00000341184.7 linkuse as main transcript	c.1005C>G	p.Gly335=	synonymous_variant	2/2	1	NM_002409.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00534

AC:

813

AN:

152250

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00137

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.00203

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000828

Gnomad FIN

AF:

0.00866

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00827

Gnomad OTH

AF:

0.00573

GnomAD3 exomes

AF:

0.00529

AC:

1320

AN:

249552

Hom.:

AF XY:

0.00519

AC XY:

702

AN XY:

135362

show subpopulations

Gnomad AFR exome

AF:

0.00155

Gnomad AMR exome

AF:

0.00208

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00219

Gnomad FIN exome

AF:

0.00982

Gnomad NFE exome

AF:

0.00801

Gnomad OTH exome

AF:

0.00768

GnomAD4 exome

AF:

0.00836

AC:

12213

AN:

1460218

Hom.:

Cov.:

AF XY:

0.00824

AC XY:

5985

AN XY:

726502

show subpopulations

Gnomad4 AFR exome

AF:

0.00125

Gnomad4 AMR exome

AF:

0.00199

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00194

Gnomad4 FIN exome

AF:

0.00992

Gnomad4 NFE exome

AF:

0.00980

Gnomad4 OTH exome

AF:

0.00831

GnomAD4 genome

AF:

0.00534

AC:

813

AN:

152368

Hom.:

Cov.:

AF XY:

0.00493

AC XY:

367

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00137

Gnomad4 AMR

AF:

0.00202

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00866

Gnomad4 NFE

AF:

0.00828

Gnomad4 OTH

AF:

0.00567

Alfa

AF:

0.00609

Hom.:

Bravo

AF:

0.00494

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00856

EpiControl

AF:

0.00812

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

May 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

9.5

DANN

Benign

0.86

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over