NM_001351288.2:c.-56-41320C>G

Variant names:

• chr12-86091043-G-C
• rs10506927
• NM_001351288.2:c.-56-41320C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351288.2(MGAT4C):​c.-56-41320C>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
• Publications: 3 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=-0.89).
• 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 rank	MANE	Protein	UniProt
MGAT4C	NM_001351288.2	c.-56-41320C>G		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.-56-41320C>G		intron_variant	Intron 1 of 4	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

African (AFR) AF: 0.379 AC: 15693 AN: 41414

American (AMR) AF: 0.144 AC: 2198 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 853 AN: 3458

East Asian (EAS) AF: 0.0540 AC: 280 AN: 5182

South Asian (SAS) AF: 0.0945 AC: 456 AN: 4824

European-Finnish (FIN) AF: 0.0873 AC: 921 AN: 10554

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10150 AN: 67788

Other (OTH) AF: 0.208 AC: 437 AN: 2102

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
PhyloP100		0.17
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: rs10506927; hg19: chr12-86484821;