chr5-180799673-A-C

Variant names:

• chr5-180799673-A-C
• rs655601
• NM_002406.4:c.-127+3007T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 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 -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT1	NM_002406.4	MANE Select	c.-127+3007T>G		intron	N/A	NP_002397.2
	MGAT1	NM_001114617.2		c.-126-6576T>G		intron	N/A	NP_001108089.1
	MGAT1	NM_001114618.1		c.-126-6576T>G		intron	N/A	NP_001108090.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MGAT1	ENST00000307826.5	TSL:1 MANE Select	c.-127+3007T>G		intron	N/A	ENSP00000311888.4
	MGAT1	ENST00000333055.8	TSL:2	c.-126-6576T>G		intron	N/A	ENSP00000332073.3
	MGAT1	ENST00000393340.7	TSL:2	c.-126-6576T>G		intron	N/A	ENSP00000377010.3

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

African (AFR) AF: 0.557 AC: 23097 AN: 41446

American (AMR) AF: 0.214 AC: 3274 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3472

East Asian (EAS) AF: 0.0964 AC: 500 AN: 5186

South Asian (SAS) AF: 0.239 AC: 1153 AN: 4824

European-Finnish (FIN) AF: 0.128 AC: 1361 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0992 AC: 6746 AN: 68004

Other (OTH) AF: 0.226 AC: 476 AN: 2108

Alfa AF: 0.141 Hom.: 10997

Bravo AF: 0.264

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.29
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs655601; hg19: chr5-180226673;