rs909674

Positions:

• chr22-39463164-C-A
• chr22-39463164-C-G
• chr22-39463164-C-T

Variant summary

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

The NM_002409.5(MGAT3):​c.-2+5607C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,226 control chromosomes in the GnomAD database, including 49,892 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 0.80 (49892 hom., cov: 34)
• Consequence: MGAT3 NM_002409.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495

Genes affected

MGAT3 (HGNC:7046): (beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase) There are believed to be over 100 different glycosyltransferases involved in the synthesis of protein-bound and lipid-bound oligosaccharides. The enzyme encoded by this gene transfers a GlcNAc residue to the beta-linked mannose of the trimannosyl core of N-linked oligosaccharides and produces a bisecting GlcNAc. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAT3	NM_002409.5	c.-2+5607C>A		intron_variant		ENST00000341184.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT3	ENST00000341184.7	c.-2+5607C>A		intron_variant		1	NM_002409.5	P1

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122239 AN: 152108 Hom.: 49825 Cov.: 34

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.804 AC: 122364 AN: 152226 Hom.: 49892 Cov.: 34 AF XY: 0.805 AC XY: 59923 AN XY: 74422

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.773

Alfa AF: 0.755 Hom.: 20141

Bravo AF: 0.815

Asia WGS AF: 0.943 AC: 3280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.7
DANN	Benign	0.87

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

Publications

LitVar

Other links and lift over

dbSNP: rs909674; hg19: chr22-39859169;