NM_001277353.2:c.95-6460A>G

Variant names:

• chr4-140488945-T-C
• rs1241050
• NM_001277353.2:c.95-6460A>G

Variant summary

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

The NM_001277353.2(MGAT4D):​c.95-6460A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,018 control chromosomes in the GnomAD database, including 47,884 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 0.79 (47884 hom., cov: 30)
• Consequence: MGAT4D NM_001277353.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655
• Publications: 4 publications found

Genes affected

MGAT4D (HGNC:43619): (MGAT4 family member D) Predicted to enable acetylglucosaminyltransferase activity. Predicted to be involved in protein N-linked glycosylation. Predicted to be located in membrane. Predicted to be active in Golgi stack; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001277353.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT4D	NM_001277353.2	MANE Select	c.95-6460A>G		intron	N/A	NP_001264282.1	A6NG13

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT4D	ENST00000511113.6	TSL:5 MANE Select	c.95-6460A>G		intron	N/A	ENSP00000421185.1	A6NG13
	MGAT4D	ENST00000503109.6	TSL:5	c.95-6460A>G		intron	N/A	ENSP00000426225.2	D6RH02
	MGAT4D	ENST00000515354.5	TSL:3	c.95-6460A>G		intron	N/A	ENSP00000423767.1	D6RCD3

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120258 AN: 151900 Hom.: 47855 Cov.: 30

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.792 AC: 120332 AN: 152018 Hom.: 47884 Cov.: 30 AF XY: 0.790 AC XY: 58696 AN XY: 74286

African (AFR) AF: 0.694 AC: 28750 AN: 41420

American (AMR) AF: 0.809 AC: 12361 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3472

East Asian (EAS) AF: 0.898 AC: 4643 AN: 5172

South Asian (SAS) AF: 0.769 AC: 3699 AN: 4812

European-Finnish (FIN) AF: 0.820 AC: 8655 AN: 10560

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56829 AN: 67996

Other (OTH) AF: 0.796 AC: 1679 AN: 2110

Alfa AF: 0.812 Hom.: 6273

Bravo AF: 0.788

Asia WGS AF: 0.806 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.55
PhyloP100		0.66
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: rs1241050; hg19: chr4-141410099;