chr12-86052783-G-A

Variant names:

• chr12-86052783-G-A
• rs7979846
• NM_001351288.2:c.-56-3060C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-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 rank	MANE	Protein	UniProt
MGAT4C	NM_001351288.2	c.-56-3060C>T		intron_variant	Intron 1 of 4	ENST00000611864.5	NP_001338217.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-56-3060C>T		intron_variant	Intron 1 of 4	5	NM_001351288.2	ENSP00000481096.1

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

African (AFR) AF: 0.399 AC: 16500 AN: 41380

American (AMR) AF: 0.157 AC: 2384 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1003 AN: 3468

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5178

South Asian (SAS) AF: 0.103 AC: 498 AN: 4820

European-Finnish (FIN) AF: 0.159 AC: 1676 AN: 10556

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11907 AN: 67874

Other (OTH) AF: 0.231 AC: 485 AN: 2102

Alfa AF: 0.189 Hom.: 12503

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
PhyloP100		4.2
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: rs7979846; hg19: chr12-86446561;