dbSNP rs11374281: MGAT4C:c.-57+71602dupG (chr12-86184636-T-TC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001351288.2(MGAT4C):c.-57+71602dupG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.66 ( 32334 hom., cov: 0)

Consequence

MGAT4C
NM_001351288.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.581

Publications

2 publications found

Variant links:

Genes affected

MGAT4C (HGNC:30871): (MGAT4 family member C) Predicted to enable acetylglucosaminyltransferase activity. Predicted to be involved in protein N-linked glycosylation. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

MGAT4C links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAT4C	NM_001351288.2 link	c.-57+71602dupG		intron_variant	Intron 1 of 4	ENST00000611864.5	NP_001338217.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000611864.5 link	c.-57+71602_-57+71603insG		intron_variant	Intron 1 of 4	5	NM_001351288.2	ENSP00000481096.1		Q9UBM8-1

Frequencies

GnomAD3 genomes

AF:

0.656

AC:

96999

AN:

147940

Hom.:

32337

Cov.:

show subpopulations

Gnomad AFR

AF:

0.539

Gnomad AMI

AF:

0.720

Gnomad AMR

AF:

0.674

Gnomad ASJ

AF:

0.635

Gnomad EAS

AF:

0.695

Gnomad SAS

AF:

0.748

Gnomad FIN

AF:

0.752

Gnomad MID

AF:

0.577

Gnomad NFE

AF:

0.699

Gnomad OTH

AF:

0.643

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

GnomAD4 genome

AF:

0.655

AC:

97018

AN:

148040

Hom.:

32334

Cov.:

AF XY:

0.659

AC XY:

47523

AN XY:

72078

show subpopulations

African (AFR)

AF:

0.539

AC:

21722

AN:

40330

American (AMR)

AF:

0.674

AC:

9948

AN:

14762

Ashkenazi Jewish (ASJ)

AF:

0.635

AC:

2200

AN:

3462

East Asian (EAS)

AF:

0.695

AC:

3507

AN:

5044

South Asian (SAS)

AF:

0.747

AC:

3499

AN:

4686

European-Finnish (FIN)

AF:

0.752

AC:

6987

AN:

9292

Middle Eastern (MID)

AF:

0.572

AC:

166

AN:

290

European-Non Finnish (NFE)

AF:

0.699

AC:

47015

AN:

67218

Other (OTH)

AF:

0.645

AC:

1322

AN:

2050

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1516

3032

4549

6065

7581

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

776

1552

2328

3104

3880

<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:

0.540

Hom.:

1289

Asia WGS

AF:

0.693

AC:

2380

AN:

3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.58

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over