5-179798324-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_014275.5(MGAT4B):c.1510+23C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 1,612,778 control chromosomes in the GnomAD database, including 1,034 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 0.033 ( 129 hom., cov: 33)

Exomes 𝑓: 0.033 ( 905 hom. )

Consequence

MGAT4B
NM_014275.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.741

Publications

25 publications found

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:

MIR1229 (HGNC:33924): (microRNA 1229) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR1229 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0332 (5061/152264) while in subpopulation AFR AF = 0.0466 (1938/41562). AF 95% confidence interval is 0.0449. There are 129 homozygotes in GnomAd4. There are 2323 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 129 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014275.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MGAT4B	NM_014275.5	MANE Select	c.1510+23C>T	intron	N/A	NP_055090.1
MIR1229	NR_031598.1		n.23C>T	non_coding_transcript_exon	Exon 1 of 1
MGAT4B	NM_054013.3		c.1555+23C>T	intron	N/A	NP_463459.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MGAT4B	ENST00000292591.12	TSL:1 MANE Select	c.1510+23C>T	intron	N/A	ENSP00000292591.7
MGAT4B	ENST00000519836.5	TSL:1	c.1112+23C>T	intron	N/A	ENSP00000430721.1
MGAT4B	ENST00000518778.5	TSL:1	c.982+23C>T	intron	N/A	ENSP00000428906.1

Frequencies

GnomAD3 genomes

AF:

0.0333

AC:

5061

AN:

152146

Hom.:

129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0467

Gnomad AMI

AF:

0.0625

Gnomad AMR

AF:

0.0234

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.0172

Gnomad FIN

AF:

0.00659

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0347

Gnomad OTH

AF:

0.0316

GnomAD2 exomes

AF:

0.0262

AC:

6533

AN:

249748

AF XY:

0.0260

show subpopulations

Gnomad AFR exome

AF:

0.0495

Gnomad AMR exome

AF:

0.0178

Gnomad ASJ exome

AF:

0.0371

Gnomad EAS exome

AF:

0.00131

Gnomad FIN exome

AF:

0.00930

Gnomad NFE exome

AF:

0.0343

Gnomad OTH exome

AF:

0.0270

GnomAD4 exome

AF:

0.0326

AC:

47679

AN:

1460514

Hom.:

905

Cov.:

AF XY:

0.0324

AC XY:

23545

AN XY:

726562

show subpopulations

African (AFR)

AF:

0.0474

AC:

1587

AN:

33466

American (AMR)

AF:

0.0179

AC:

802

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.0389

AC:

1017

AN:

26132

East Asian (EAS)

AF:

0.00186

AC:

AN:

39696

South Asian (SAS)

AF:

0.0166

AC:

1436

AN:

86250

European-Finnish (FIN)

AF:

0.0106

AC:

552

AN:

52308

Middle Eastern (MID)

AF:

0.0387

AC:

223

AN:

5768

European-Non Finnish (NFE)

AF:

0.0359

AC:

39863

AN:

1111808

Other (OTH)

AF:

0.0352

AC:

2125

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

2715

5430

8146

10861

13576

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1508

3016

4524

6032

7540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0332

AC:

5061

AN:

152264

Hom.:

129

Cov.:

AF XY:

0.0312

AC XY:

2323

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0466

AC:

1938

AN:

41562

American (AMR)

AF:

0.0234

AC:

358

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0323

AC:

112

AN:

3472

East Asian (EAS)

AF:

0.00213

AC:

AN:

5166

South Asian (SAS)

AF:

0.0170

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00659

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0347

AC:

2360

AN:

67988

Other (OTH)

AF:

0.0313

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

253

506

759

1012

1265

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

168

224

280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0356

Hom.:

Bravo

AF:

0.0349

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.99

(source)

DANN

Benign

0.74

PhyloP100

-0.74

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over