rs655601

chr5-180799673-A-Cchr5-180799673-A-T

Variant summary

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

The NM_002406.4(MGAT1):c.-127+3007T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,132 control chromosomes in the GnomAD database, including 7,539 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 0.24 (7539 hom., cov: 32)
• Consequence: MGAT1 NM_002406.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

Genes affected

MGAT1 (HGNC:7044): (alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase) There are believed to be over 100 different glycosyltransferases involved in the synthesis of protein-bound and lipid-bound oligosaccharides. UDP-N-acetylglucosamine:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I is a medial-Golgi enzyme essential for the synthesis of hybrid and complex N-glycans. The protein, encoded by a single exon, shows typical features of a type II transmembrane protein. The protein is believed to be essential for normal embryogenesis. Several variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAT1	NM_002406.4	c.-127+3007T>G		intron_variant		ENST00000307826.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT1	ENST00000307826.5	c.-127+3007T>G		intron_variant		1	NM_002406.4	P1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37106 AN: 152014 Hom.: 7519 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0964

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.244 AC: 37186 AN: 152132 Hom.: 7539 Cov.: 32 AF XY: 0.243 AC XY: 18042 AN XY: 74382

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0964

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0992

Gnomad4 OTH AF: 0.226

Alfa AF: 0.120 Hom.: 3499

Bravo AF: 0.264

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.9
Dann	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs655601; hg19: chr5-180226673;