rs1586938

Variant names:

• chr12-86108373-T-G
• rs1586938
• NM_001351288.2:c.-56-58650A>C

Variant summary

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

The NM_001351288.2(MGAT4C):​c.-56-58650A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0347 in 152,224 control chromosomes in the GnomAD database, including 291 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 0.035 (291 hom., cov: 32)
• Consequence: MGAT4C NM_001351288.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAT4C	NM_001351288.2	c.-56-58650A>C		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.-56-58650A>C		intron_variant	Intron 1 of 4	5	NM_001351288.2	ENSP00000481096.1

Frequencies

GnomAD3 genomes AF: 0.0345 AC: 5244 AN: 152104 Hom.: 286 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0589

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.0168

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.0302

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

GnomAD4 genome AF: 0.0347 AC: 5277 AN: 152224 Hom.: 291 Cov.: 32 AF XY: 0.0384 AC XY: 2859 AN XY: 74412

African (AFR) AF: 0.0321 AC: 1334 AN: 41560

American (AMR) AF: 0.0591 AC: 903 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1449 AN: 5154

South Asian (SAS) AF: 0.0967 AC: 466 AN: 4820

European-Finnish (FIN) AF: 0.0168 AC: 178 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0116 AC: 791 AN: 68022

Other (OTH) AF: 0.0318 AC: 67 AN: 2110

Alfa AF: 0.0228 Hom.: 13

Bravo AF: 0.0388

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.71
PhyloP100		0.31
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: rs1586938; hg19: chr12-86502151;