rs7975457

Variant names:

• chr12-86016626-G-A
• rs7975457
• NM_001351288.2:c.-6-27074C>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.-6-27074C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,006 control chromosomes in the GnomAD database, including 15,936 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 0.45 (15936 hom., cov: 32)
• Consequence: MGAT4C NM_001351288.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• 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]

ENSG00000257897 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MGAT4C	NM_001351288.2	c.-6-27074C>T		intron_variant	Intron 2 of 4	ENST00000611864.5	NP_001338217.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-6-27074C>T		intron_variant	Intron 2 of 4	5	NM_001351288.2	ENSP00000481096.1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67700 AN: 151888 Hom.: 15910 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.0833

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.446 AC: 67778 AN: 152006 Hom.: 15936 Cov.: 32 AF XY: 0.435 AC XY: 32288 AN XY: 74280

African (AFR) AF: 0.532 AC: 22041 AN: 41444

American (AMR) AF: 0.372 AC: 5683 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1821 AN: 3468

East Asian (EAS) AF: 0.0833 AC: 431 AN: 5172

South Asian (SAS) AF: 0.185 AC: 891 AN: 4816

European-Finnish (FIN) AF: 0.422 AC: 4456 AN: 10554

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30928 AN: 67956

Other (OTH) AF: 0.446 AC: 943 AN: 2112

Alfa AF: 0.441 Hom.: 9747

Bravo AF: 0.448

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.22
PhyloP100		-0.18
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: rs7975457; hg19: chr12-86410404;