2-98688331-A-G

Variant names:

• chr2-98688331-A-G
• rs885036
• NM_012214.3:c.95-9860T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MGAT4A	NM_012214.3	c.95-9860T>C		intron_variant	Intron 2 of 15	ENST00000393487.6	NP_036346.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGAT4A	ENST00000393487.6	c.95-9860T>C		intron_variant	Intron 2 of 15	5	NM_012214.3	ENSP00000377127.1

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

African (AFR) AF: 0.763 AC: 31600 AN: 41416

American (AMR) AF: 0.537 AC: 8201 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1886 AN: 5144

South Asian (SAS) AF: 0.490 AC: 2362 AN: 4816

European-Finnish (FIN) AF: 0.371 AC: 3912 AN: 10554

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33823 AN: 67906

Other (OTH) AF: 0.550 AC: 1157 AN: 2104

Alfa AF: 0.514 Hom.: 59657

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
PhyloP100		-0.68
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: rs885036; hg19: chr2-99304794;