rs11374281

Variant names:

• chr12-86184636-T-TC
• rs11374281
• NM_001351288.2:c.-57+71602dupG

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 2 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351288.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT4C	NM_001351288.2	MANE Select	c.-57+71602dupG		intron	N/A	NP_001338217.1	Q9UBM8-1
	MGAT4C	NM_001351282.2		c.-31+71602dupG		intron	N/A	NP_001338211.1
	MGAT4C	NM_001351283.2		c.-74+71602dupG		intron	N/A	NP_001338212.1	Q9UBM8-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT4C	ENST00000611864.5	TSL:5 MANE Select	c.-57+71602_-57+71603insG		intron	N/A	ENSP00000481096.1	Q9UBM8-1
	MGAT4C	ENST00000621808.5	TSL:1	c.-176-134914_-176-134913insG		intron	N/A	ENSP00000478300.1	Q9UBM8-1
	MGAT4C	ENST00000547225.5	TSL:1	c.-153+71602_-153+71603insG		intron	N/A	ENSP00000449172.1	F8VWY2

Frequencies

GnomAD3 genomes AF: 0.656 AC: 96999 AN: 147940 Hom.: 32337 Cov.: 0

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.: 0 AF XY: 0.659 AC XY: 47523 AN XY: 72078

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

Alfa AF: 0.540 Hom.: 1289

Asia WGS AF: 0.693 AC: 2380 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.58
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11374281; hg19: chr12-86578414;