12-86004592-C-G

Variant names:

• chr12-86004592-C-G
• rs7313373
• NM_001351288.2:c.-6-15040G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351288.2(MGAT4C):​c.-6-15040G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,892 control chromosomes in the GnomAD database, including 16,087 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 0.45 (16087 hom., cov: 32)
• Consequence: MGAT4C NM_001351288.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 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.-6-15040G>C		intron	N/A	NP_001338217.1	Q9UBM8-1
	MGAT4C	NM_001351282.2		c.21-3011G>C		intron	N/A	NP_001338211.1
	MGAT4C	NM_001351283.2		c.82-15040G>C		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.-6-15040G>C		intron	N/A	ENSP00000481096.1	Q9UBM8-1
	MGAT4C	ENST00000621808.5	TSL:1	c.-6-15040G>C		intron	N/A	ENSP00000478300.1	Q9UBM8-1
	MGAT4C	ENST00000547225.5	TSL:1	c.-6-15040G>C		intron	N/A	ENSP00000449172.1	F8VWY2

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67949 AN: 151774 Hom.: 16056 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.0796

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.448 AC: 68033 AN: 151892 Hom.: 16087 Cov.: 32 AF XY: 0.436 AC XY: 32379 AN XY: 74192

African (AFR) AF: 0.540 AC: 22342 AN: 41410

American (AMR) AF: 0.373 AC: 5682 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1821 AN: 3464

East Asian (EAS) AF: 0.0796 AC: 410 AN: 5150

South Asian (SAS) AF: 0.184 AC: 885 AN: 4812

European-Finnish (FIN) AF: 0.422 AC: 4439 AN: 10528

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30925 AN: 67964

Other (OTH) AF: 0.449 AC: 948 AN: 2110

Alfa AF: 0.339 Hom.: 910

Bravo AF: 0.450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.29
PhyloP100		-2.5
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: rs7313373; hg19: chr12-86398370;