12-86748104-C-G

Position:

• chr12-86748104-C-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+90562G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0439 in 151,564 control chromosomes in the GnomAD database, including 340 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 0.044 (340 hom., cov: 32)
• Consequence: MGAT4C NM_013244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAT4C	NM_001351285.2	c.-326-20863G>C		intron_variant			NP_001338214.1
MGAT4C	NM_001351286.2	c.-261-20863G>C		intron_variant			NP_001338215.1
MGAT4C	NM_013244.5	c.-229+90562G>C		intron_variant			NP_037376.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000621808.5	c.-381-20863G>C		intron_variant		1		ENSP00000478300.1
MGAT4C	ENST00000548651.6	c.-261-20863G>C		intron_variant		5		ENSP00000447253.1
ENSG00000258185	ENST00000550014.1	n.334-20863G>C		intron_variant		5
MGAT4C	ENST00000551921.2	n.240-20863G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0438 AC: 6631 AN: 151446 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0211

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.00274

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0312

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

GnomAD4 genome AF: 0.0439 AC: 6650 AN: 151564 Hom.: 340 Cov.: 32 AF XY: 0.0417 AC XY: 3087 AN XY: 74054

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0210

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0129

Gnomad4 FIN AF: 0.00274

Gnomad4 NFE AF: 0.0146

Gnomad4 OTH AF: 0.0309

Alfa AF: 0.00956 Hom.: 10

Bravo AF: 0.0492

Asia WGS AF: 0.0150 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.78
DANN	Benign	0.35

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: rs10492295; hg19: chr12-87141881;