rs2070924

Variant names:

• chr5-180791831-G-A
• rs2070924
• NM_002406.4:c.1141C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-180791831-G-A
• chr5-180791831-G-C
• chr5-180791831-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_002406.4(MGAT1):​c.1141C>T​(p.Leu381Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0534 in 1,614,124 control chromosomes in the GnomAD database, including 3,249 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 0.068 (436 hom., cov: 33)
  • Exomes 𝑓: 0.052 (2813 hom.)
• Consequence: MGAT1 NM_002406.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 17 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP7: Synonymous conserved (PhyloP=1.39 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.19 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.1141C>T	p.Leu381Leu	synonymous	Exon 2 of 2	NP_002397.2
	MGAT1	NM_001114617.2		c.1141C>T	p.Leu381Leu	synonymous	Exon 3 of 3	NP_001108089.1
	MGAT1	NM_001114618.1		c.1141C>T	p.Leu381Leu	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.1141C>T	p.Leu381Leu	synonymous	Exon 2 of 2	ENSP00000311888.4
	MGAT1	ENST00000333055.8	TSL:2	c.1141C>T	p.Leu381Leu	synonymous	Exon 3 of 3	ENSP00000332073.3
	MGAT1	ENST00000393340.7	TSL:2	c.1141C>T	p.Leu381Leu	synonymous	Exon 3 of 3	ENSP00000377010.3

Frequencies

GnomAD3 genomes AF: 0.0675 AC: 10265 AN: 152130 Hom.: 434 Cov.: 33

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0432

Gnomad OTH AF: 0.0636

GnomAD2 exomes AF: 0.0703 AC: 17668 AN: 251352 AF XY: 0.0718

Gnomad AFR exome AF: 0.0894

Gnomad AMR exome AF: 0.0431

Gnomad ASJ exome AF: 0.0339

Gnomad EAS exome AF: 0.222

Gnomad FIN exome AF: 0.0825

Gnomad NFE exome AF: 0.0423

Gnomad OTH exome AF: 0.0550

GnomAD4 exome AF: 0.0520 AC: 75987 AN: 1461876 Hom.: 2813 Cov.: 36 AF XY: 0.0536 AC XY: 39006 AN XY: 727240

African (AFR) AF: 0.0908 AC: 3039 AN: 33480

American (AMR) AF: 0.0443 AC: 1982 AN: 44724

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

East Asian (EAS) AF: 0.193 AC: 7666 AN: 39700

South Asian (SAS) AF: 0.107 AC: 9267 AN: 86258

European-Finnish (FIN) AF: 0.0807 AC: 4309 AN: 53412

Middle Eastern (MID) AF: 0.0756 AC: 436 AN: 5768

European-Non Finnish (NFE) AF: 0.0405 AC: 44984 AN: 1112002

Other (OTH) AF: 0.0560 AC: 3382 AN: 60396

GnomAD4 genome AF: 0.0675 AC: 10279 AN: 152248 Hom.: 436 Cov.: 33 AF XY: 0.0717 AC XY: 5337 AN XY: 74440

African (AFR) AF: 0.0897 AC: 3725 AN: 41530

American (AMR) AF: 0.0439 AC: 672 AN: 15304

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

East Asian (EAS) AF: 0.200 AC: 1034 AN: 5166

South Asian (SAS) AF: 0.120 AC: 579 AN: 4818

European-Finnish (FIN) AF: 0.0917 AC: 974 AN: 10620

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0433 AC: 2942 AN: 68018

Other (OTH) AF: 0.0658 AC: 139 AN: 2114

Alfa AF: 0.0481 Hom.: 454

Bravo AF: 0.0660

Asia WGS AF: 0.142 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	8.8
DANN	Benign	0.85
PhyloP100		1.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs2070924; hg19: chr5-180218831; COSMIC: COSV57133073; COSMIC: COSV57133073;