12-86004592-C-G

Position:

• chr12-86004592-C-G

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAT4C	NM_001351288.2	c.-6-15040G>C		intron_variant		ENST00000611864.5	NP_001338217.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-6-15040G>C		intron_variant		5	NM_001351288.2	ENSP00000481096.1

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

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.0796

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.449

Alfa AF: 0.339 Hom.: 910

Bravo AF: 0.450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.29

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: rs7313373; hg19: chr12-86398370;