Variant rs166624 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014275.5(MGAT4B):c.720-27C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,611,510 control chromosomes in the GnomAD database, including 26,414 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 0.23 ( 4591 hom., cov: 32)

Exomes 𝑓: 0.17 ( 21823 hom. )

Consequence

MGAT4B
NM_014275.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0980

Variant links:

Genes affected

MGAT4B (HGNC:7048): (alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B) 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 A, 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]

MGAT4B links:

MGAT4B (HGNC:):

MGAT4B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
MGAT4B	NM_014275.5 linkuse as main transcript	c.720-27C>A	intron_variant	ENST00000292591.12	NP_055090.1	Q9UQ53-1
MGAT4B	NM_054013.3 linkuse as main transcript	c.765-27C>A	intron_variant		NP_463459.1	Q9UQ53-3
MGAT4B	XM_024454349.2 linkuse as main transcript	c.285-27C>A	intron_variant		XP_024310117.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT4B	ENST00000292591.12 linkuse as main transcript	c.720-27C>A		intron_variant		1	NM_014275.5	ENSP00000292591.7		Q9UQ53-1

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34333

AN:

151894

Hom.:

4591

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.237

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.218

GnomAD3 exomes

AF:

0.180

AC:

44761

AN:

249240

Hom.:

4540

AF XY:

0.175

AC XY:

23611

AN XY:

135226

show subpopulations

Gnomad AFR exome

AF:

0.382

Gnomad AMR exome

AF:

0.168

Gnomad ASJ exome

AF:

0.195

Gnomad EAS exome

AF:

0.253

Gnomad SAS exome

AF:

0.145

Gnomad FIN exome

AF:

0.154

Gnomad NFE exome

AF:

0.155

Gnomad OTH exome

AF:

0.182

GnomAD4 exome

AF:

0.167

AC:

243473

AN:

1459498

Hom.:

21823

Cov.:

AF XY:

0.166

AC XY:

120414

AN XY:

726144

show subpopulations

Gnomad4 AFR exome

AF:

0.385

Gnomad4 AMR exome

AF:

0.173

Gnomad4 ASJ exome

AF:

0.191

Gnomad4 EAS exome

AF:

0.270

Gnomad4 SAS exome

AF:

0.145

Gnomad4 FIN exome

AF:

0.148

Gnomad4 NFE exome

AF:

0.157

Gnomad4 OTH exome

AF:

0.182

GnomAD4 genome

AF:

0.226

AC:

34355

AN:

152012

Hom.:

4591

Cov.:

AF XY:

0.222

AC XY:

16497

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.379

Gnomad4 AMR

AF:

0.195

Gnomad4 ASJ

AF:

0.205

Gnomad4 EAS

AF:

0.237

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.152

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.216

Alfa

AF:

0.173

Hom.:

2757

Bravo

AF:

0.239

Asia WGS

AF:

0.194

AC:

671

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.0

DANN

Benign

0.77

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over