12-86091043-G-C

Position:

• chr12-86091043-G-C

Variant summary

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

The NM_001351288.2(MGAT4C):​c.-56-41320C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,740 control chromosomes in the GnomAD database, including 4,227 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 0.21 (4227 hom., cov: 32)
• Consequence: MGAT4C NM_001351288.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

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]

MGAT4C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAT4C	NM_001351288.2	c.-56-41320C>G		intron_variant		ENST00000611864.5	NP_001338217.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-56-41320C>G		intron_variant		5	NM_001351288.2	ENSP00000481096.1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31218 AN: 151622 Hom.: 4221 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.0537

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0873

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.206 AC: 31232 AN: 151740 Hom.: 4227 Cov.: 32 AF XY: 0.199 AC XY: 14797 AN XY: 74178

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.0540

Gnomad4 SAS AF: 0.0945

Gnomad4 FIN AF: 0.0873

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.208

Alfa AF: 0.188 Hom.: 427

Bravo AF: 0.220

Asia WGS AF: 0.0910 AC: 314 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.30

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: rs10506927; hg19: chr12-86484821;