rs10506928

Variant names:

• chr12-86107598-G-A
• rs10506928
• NM_001351288.2:c.-56-57875C>T

Variant summary

Our verdict is Benign. The variant received -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
• 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MGAT4C	NM_001351288.2	c.-56-57875C>T		intron_variant	Intron 1 of 4	ENST00000611864.5	NP_001338217.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-56-57875C>T		intron_variant	Intron 1 of 4	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

African (AFR) AF: 0.0211 AC: 875 AN: 41504

American (AMR) AF: 0.104 AC: 1592 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0408 AC: 197 AN: 4824

European-Finnish (FIN) AF: 0.0535 AC: 566 AN: 10578

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7166 AN: 67970

Other (OTH) AF: 0.111 AC: 235 AN: 2112

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
PhyloP100		-0.65
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: rs10506928; hg19: chr12-86501376; COSMIC: COSV73453309;