chr4-140466284-C-T

Variant names:

• chr4-140466284-C-T
• rs1594468
• NM_001277353.2:c.573-1275G>A

Variant summary

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

The NM_001277353.2(MGAT4D):​c.573-1275G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,910 control chromosomes in the GnomAD database, including 4,915 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 0.25 (4915 hom., cov: 32)
• Consequence: MGAT4D NM_001277353.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.361 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.573-1275G>A		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.573-1275G>A		intron	N/A	ENSP00000421185.1	A6NG13
	MGAT4D	ENST00000503109.6	TSL:5	c.573-1275G>A		intron	N/A	ENSP00000426225.2	D6RH02
	MGAT4D	ENST00000515354.5	TSL:3	c.254-9565G>A		intron	N/A	ENSP00000423767.1	D6RCD3

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38160 AN: 151792 Hom.: 4918 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.251 AC: 38175 AN: 151910 Hom.: 4915 Cov.: 32 AF XY: 0.256 AC XY: 19044 AN XY: 74262

African (AFR) AF: 0.236 AC: 9798 AN: 41446

American (AMR) AF: 0.319 AC: 4872 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3466

East Asian (EAS) AF: 0.284 AC: 1470 AN: 5170

South Asian (SAS) AF: 0.375 AC: 1809 AN: 4820

European-Finnish (FIN) AF: 0.239 AC: 2520 AN: 10566

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15808 AN: 67870

Other (OTH) AF: 0.257 AC: 543 AN: 2110

Alfa AF: 0.244 Hom.: 9034

Bravo AF: 0.256

Asia WGS AF: 0.340 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.5
DANN	Benign	0.64
PhyloP100		-1.4
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: rs1594468; hg19: chr4-141387438;