rs10506928

Positions:

• chr12-86107598-G-A

Variant summary

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

The NM_001351288.2(MGAT4C):​c.-56-57875C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0754 in 152,108 control chromosomes in the GnomAD database, including 588 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 0.075 (588 hom., cov: 32)
• Consequence: MGAT4C NM_001351288.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAT4C	NM_001351288.2	c.-56-57875C>T		intron_variant		ENST00000611864.5	NP_001338217.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-56-57875C>T		intron_variant		5	NM_001351288.2	ENSP00000481096.1

Frequencies

GnomAD3 genomes AF: 0.0755 AC: 11475 AN: 151992 Hom.: 589 Cov.: 32

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0754 AC: 11468 AN: 152108 Hom.: 588 Cov.: 32 AF XY: 0.0727 AC XY: 5405 AN XY: 74332

Gnomad4 AFR AF: 0.0211

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0849 Hom.: 85

Bravo AF: 0.0803

Asia WGS AF: 0.0210 AC: 71 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.61
DANN	Benign	0.44

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: rs10506928; hg19: chr12-86501376; COSMIC: COSV73453309;