rs885036

chr2-98688331-A-G

Variant summary

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

The NM_012214.3(MGAT4A):c.95-9860T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,898 control chromosomes in the GnomAD database, including 25,467 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 0.56 (25467 hom., cov: 31)
• Consequence: MGAT4A NM_012214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676

Genes affected

MGAT4A (HGNC:7047): (alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A) This gene encodes a key glycosyltransferase that regulates the formation of tri- and multiantennary branching structures in the Golgi apparatus. The encoded protein, in addition to the related isoenzyme B, catalyzes the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc in a beta-1,4 linkage to the Man-alpha-1,3-Man-beta-1,4-GlcNAc arm of R-Man-alpha-1,6(GlcNAc-beta-1,2-Man-alpha-1,3)Man-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1-Asn. The encoded protein may play a role in regulating the availability of serum glycoproteins, oncogenesis, and differentiation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MGAT4A	NM_012214.3	c.95-9860T>C		intron_variant		ENST00000393487.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MGAT4A	ENST00000393487.6	c.95-9860T>C		intron_variant		5	NM_012214.3	P1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85287 AN: 151780 Hom.: 25417 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.562 AC: 85394 AN: 151898 Hom.: 25467 Cov.: 31 AF XY: 0.556 AC XY: 41240 AN XY: 74238

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.550

Alfa AF: 0.507 Hom.: 26148

Bravo AF: 0.582

Asia WGS AF: 0.447 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.69
Dann	Benign	0.39

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: rs885036; hg19: chr2-99304794;