rs1586938

chr12-86108373-T-G

Variant summary

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

The NM_001351288.2(MGAT4C):c.-56-58650A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0347 in 152,224 control chromosomes in the GnomAD database, including 291 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 0.035 (291 hom., cov: 32)
• Consequence: MGAT4C NM_001351288.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAT4C	NM_001351288.2	c.-56-58650A>C		intron_variant		ENST00000611864.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-56-58650A>C		intron_variant		5	NM_001351288.2	P1

Frequencies

GnomAD3 genomes AF: 0.0345 AC: 5244 AN: 152104 Hom.: 286 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0589

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.0168

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.0302

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

GnomAD4 genome AF: 0.0347 AC: 5277 AN: 152224 Hom.: 291 Cov.: 32 AF XY: 0.0384 AC XY: 2859 AN XY: 74412

Gnomad4 AFR AF: 0.0321

Gnomad4 AMR AF: 0.0591

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.0967

Gnomad4 FIN AF: 0.0168

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.0228 Hom.: 13

Bravo AF: 0.0388

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.9
Dann	Benign	0.71

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: rs1586938; hg19: chr12-86502151;