rs9669353

Positions:

• chr12-86054400-G-A
• chr12-86054400-G-C

Variant summary

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

The NM_001351288.2(MGAT4C):​c.-56-4677C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 151,882 control chromosomes in the GnomAD database, including 49,492 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 0.80 (49492 hom., cov: 31)
• Consequence: MGAT4C NM_001351288.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAT4C	NM_001351288.2	c.-56-4677C>T		intron_variant		ENST00000611864.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT4C	ENST00000611864.5	c.-56-4677C>T		intron_variant		5	NM_001351288.2	P1

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121632 AN: 151764 Hom.: 49445 Cov.: 31

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.802 AC: 121737 AN: 151882 Hom.: 49492 Cov.: 31 AF XY: 0.807 AC XY: 59929 AN XY: 74226

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.794

Alfa AF: 0.769 Hom.: 7693

Bravo AF: 0.810

Asia WGS AF: 0.931 AC: 3238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.20

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: rs9669353; hg19: chr12-86448178;