rs7979846

chr12-86052783-G-Achr12-86052783-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351288.2(MGAT4C):c.-56-3060C>T variant causes a intron change. The variant allele was found at a frequency of 0.23 in 151,772 control chromosomes in the GnomAD database, including 4,939 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 0.23 (4939 hom., cov: 32)
• Consequence: MGAT4C NM_001351288.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.19

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAT4C	NM_001351288.2	c.-56-3060C>T		intron_variant		ENST00000611864.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-56-3060C>T		intron_variant		5	NM_001351288.2	P1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34951 AN: 151654 Hom.: 4933 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.230 AC: 34983 AN: 151772 Hom.: 4939 Cov.: 32 AF XY: 0.226 AC XY: 16743 AN XY: 74178

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.0521

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.231

Alfa AF: 0.178 Hom.: 4808

Bravo AF: 0.239

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	15
Dann	Benign	0.37

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: rs7979846; hg19: chr12-86446561;