4-140488945-T-C

Position:

• chr4-140488945-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

MGAT4D (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAT4D	NM_001277353.2	c.95-6460A>G		intron_variant		ENST00000511113.6	NP_001264282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT4D	ENST00000511113.6	c.95-6460A>G		intron_variant		5	NM_001277353.2	ENSP00000421185.1

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

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.796

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.55

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: rs1241050; hg19: chr4-141410099;