12-86826312-T-G

Position:

• chr12-86826312-T-G

Variant summary

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

The NM_013244.5(MGAT4C):​c.-229+12354A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,118 control chromosomes in the GnomAD database, including 32,056 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 0.64 (32056 hom., cov: 31)
• Consequence: MGAT4C NM_013244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

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]

ENSG00000258185 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAT4C	NM_001351285.2	c.-327+12354A>C		intron_variant			NP_001338214.1
MGAT4C	NM_001351286.2	c.-262+12354A>C		intron_variant			NP_001338215.1
MGAT4C	NM_013244.5	c.-229+12354A>C		intron_variant			NP_037376.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000621808.5	c.-382+12354A>C		intron_variant		1		ENSP00000478300.1
MGAT4C	ENST00000548651.6	c.-262+12354A>C		intron_variant		5		ENSP00000447253.1
ENSG00000258185	ENST00000550014.1	n.333+12354A>C		intron_variant		5
MGAT4C	ENST00000551921.2	n.239+12354A>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96348 AN: 151000 Hom.: 32016 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.638 AC: 96445 AN: 151118 Hom.: 32056 Cov.: 31 AF XY: 0.638 AC XY: 47112 AN XY: 73792

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.657

Alfa AF: 0.698 Hom.: 16360

Bravo AF: 0.630

Asia WGS AF: 0.515 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.49

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: rs2130177; hg19: chr12-87220089;