chr12-86826312-T-G

Variant names:

• chr12-86826312-T-G
• rs2130177
• ENST00000621808.5:c.-382+12354A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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]

ENSG00000258185 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013244.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT4C	NM_001351285.2		c.-327+12354A>C		intron	N/A	NP_001338214.1	Q9UBM8-1
	MGAT4C	NM_001351286.2		c.-262+12354A>C		intron	N/A	NP_001338215.1	Q9UBM8-1
	MGAT4C	NM_013244.5		c.-229+12354A>C		intron	N/A	NP_037376.2	Q9UBM8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT4C	ENST00000621808.5	TSL:1	c.-382+12354A>C		intron	N/A	ENSP00000478300.1	Q9UBM8-1
	MGAT4C	ENST00000548651.6	TSL:5	c.-262+12354A>C		intron	N/A	ENSP00000447253.1	Q9UBM8-1
	ENSG00000258185	ENST00000550014.1	TSL:5	n.333+12354A>C		intron	N/A

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

African (AFR) AF: 0.467 AC: 19268 AN: 41292

American (AMR) AF: 0.724 AC: 10919 AN: 15090

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2565 AN: 3444

East Asian (EAS) AF: 0.331 AC: 1695 AN: 5116

South Asian (SAS) AF: 0.675 AC: 3253 AN: 4818

European-Finnish (FIN) AF: 0.730 AC: 7716 AN: 10570

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 48783 AN: 67486

Other (OTH) AF: 0.657 AC: 1379 AN: 2098

Alfa AF: 0.684 Hom.: 23862

Bravo AF: 0.630

Asia WGS AF: 0.515 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.49
PhyloP100		-2.0
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: rs2130177; hg19: chr12-87220089;