chr5-180791820-C-A

Variant names:

• chr5-180791820-C-A
• rs2070925
• NM_002406.4:c.1152G>T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_002406.4(MGAT1):​c.1152G>T​(p.Val384Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0545 in 1,614,172 control chromosomes in the GnomAD database, including 3,315 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 0.075 (550 hom., cov: 33)
  • Exomes 𝑓: 0.052 (2765 hom.)
• Consequence: MGAT1 NM_002406.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BP7: Synonymous conserved (PhyloP=0.35 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002406.4. 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
	MGAT1	NM_002406.4	MANE Select	c.1152G>T	p.Val384Val	synonymous	Exon 2 of 2	NP_002397.2
	MGAT1	NM_001114617.2		c.1152G>T	p.Val384Val	synonymous	Exon 3 of 3	NP_001108089.1
	MGAT1	NM_001114618.1		c.1152G>T	p.Val384Val	synonymous	Exon 3 of 3	NP_001108090.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT1	ENST00000307826.5	TSL:1 MANE Select	c.1152G>T	p.Val384Val	synonymous	Exon 2 of 2	ENSP00000311888.4
	MGAT1	ENST00000333055.8	TSL:2	c.1152G>T	p.Val384Val	synonymous	Exon 3 of 3	ENSP00000332073.3
	MGAT1	ENST00000393340.7	TSL:2	c.1152G>T	p.Val384Val	synonymous	Exon 3 of 3	ENSP00000377010.3

Frequencies

GnomAD3 genomes AF: 0.0754 AC: 11468 AN: 152178 Hom.: 548 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0485

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0434

Gnomad OTH AF: 0.0713

GnomAD2 exomes AF: 0.0715 AC: 17966 AN: 251354 AF XY: 0.0724

Gnomad AFR exome AF: 0.117

Gnomad AMR exome AF: 0.0453

Gnomad ASJ exome AF: 0.0339

Gnomad EAS exome AF: 0.209

Gnomad FIN exome AF: 0.0821

Gnomad NFE exome AF: 0.0426

Gnomad OTH exome AF: 0.0554

GnomAD4 exome AF: 0.0523 AC: 76444 AN: 1461878 Hom.: 2765 Cov.: 36 AF XY: 0.0538 AC XY: 39128 AN XY: 727240

African (AFR) AF: 0.118 AC: 3965 AN: 33480

American (AMR) AF: 0.0469 AC: 2096 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.0353 AC: 922 AN: 26136

East Asian (EAS) AF: 0.165 AC: 6552 AN: 39700

South Asian (SAS) AF: 0.107 AC: 9232 AN: 86256

European-Finnish (FIN) AF: 0.0801 AC: 4281 AN: 53418

Middle Eastern (MID) AF: 0.0813 AC: 469 AN: 5768

European-Non Finnish (NFE) AF: 0.0409 AC: 45436 AN: 1112004

Other (OTH) AF: 0.0578 AC: 3491 AN: 60396

GnomAD4 genome AF: 0.0754 AC: 11482 AN: 152294 Hom.: 550 Cov.: 33 AF XY: 0.0793 AC XY: 5905 AN XY: 74460

African (AFR) AF: 0.118 AC: 4897 AN: 41566

American (AMR) AF: 0.0487 AC: 745 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3472

East Asian (EAS) AF: 0.187 AC: 969 AN: 5170

South Asian (SAS) AF: 0.120 AC: 578 AN: 4820

European-Finnish (FIN) AF: 0.0911 AC: 967 AN: 10610

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2956 AN: 68028

Other (OTH) AF: 0.0734 AC: 155 AN: 2112

Alfa AF: 0.0554 Hom.: 580

Bravo AF: 0.0752

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	7.2
DANN	Benign	0.84
PhyloP100		0.35
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: rs2070925; hg19: chr5-180218820; COSMIC: COSV57133062; COSMIC: COSV57133062;