rs11374281

chr12-86184636-T-TC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001351288.2(MGAT4C):c.-57+71602_-57+71603insG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 148,040 control chromosomes in the GnomAD database, including 32,334 homozygotes. 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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MGAT4C	NM_001351288.2	c.-57+71602_-57+71603insG		intron_variant		ENST00000611864.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-57+71602_-57+71603insG		intron_variant		5	NM_001351288.2	P1

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

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.645

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

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

Other links and lift over

dbSNP: rs11374281; hg19: chr12-86578414;