chr12-86016626-G-A

Position:

• chr12-86016626-G-A

Variant summary

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

The NM_001351288.2(MGAT4C):​c.-6-27074C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,006 control chromosomes in the GnomAD database, including 15,936 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 (15936 hom., cov: 32)
• Consequence: MGAT4C NM_001351288.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAT4C	NM_001351288.2	c.-6-27074C>T		intron_variant		ENST00000611864.5	NP_001338217.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-6-27074C>T		intron_variant		5	NM_001351288.2	ENSP00000481096	P1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67700 AN: 151888 Hom.: 15910 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.0833

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.446 AC: 67778 AN: 152006 Hom.: 15936 Cov.: 32 AF XY: 0.435 AC XY: 32288 AN XY: 74280

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.0833

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.446

Alfa AF: 0.439 Hom.: 8903

Bravo AF: 0.448

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.22

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: rs7975457; hg19: chr12-86410404;