12-86751446-A-G

Variant names:

• chr12-86751446-A-G
• rs2217235
• ENST00000621808.5:c.-381-24205T>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+87220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,804 control chromosomes in the GnomAD database, including 17,345 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 0.47 (17345 hom., cov: 32)
• Consequence: MGAT4C NM_013244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 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.-326-24205T>C		intron	N/A	NP_001338214.1	Q9UBM8-1
	MGAT4C	NM_001351286.2		c.-261-24205T>C		intron	N/A	NP_001338215.1	Q9UBM8-1
	MGAT4C	NM_013244.5		c.-229+87220T>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.-381-24205T>C		intron	N/A	ENSP00000478300.1	Q9UBM8-1
	MGAT4C	ENST00000548651.6	TSL:5	c.-261-24205T>C		intron	N/A	ENSP00000447253.1	Q9UBM8-1
	ENSG00000258185	ENST00000550014.1	TSL:5	n.334-24205T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71942 AN: 151686 Hom.: 17324 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.474 AC: 72005 AN: 151804 Hom.: 17345 Cov.: 32 AF XY: 0.470 AC XY: 34838 AN XY: 74148

African (AFR) AF: 0.518 AC: 21474 AN: 41420

American (AMR) AF: 0.381 AC: 5801 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1815 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2383 AN: 5124

South Asian (SAS) AF: 0.464 AC: 2240 AN: 4824

European-Finnish (FIN) AF: 0.393 AC: 4156 AN: 10574

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.480 AC: 32594 AN: 67868

Other (OTH) AF: 0.448 AC: 942 AN: 2104

Alfa AF: 0.478 Hom.: 6177

Bravo AF: 0.474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.33
PhyloP100		-0.72
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2217235;

hg19: chr12-87145223;