Variant chr17-76872805-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_198955.1(MGAT5B):c.56C>T(p.Thr19Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00515 in 1,614,078 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0043 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0052 ( 36 hom. )

Consequence

MGAT5B
NM_198955.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.100

Variant links:

Genes affected

MGAT5B (HGNC:24140): (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase B) Enables alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity and manganese ion binding activity. Involved in protein O-linked glycosylation via serine. Predicted to be located in Golgi membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

MGAT5B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0034640431).

BP6

Variant 17-76872805-C-T is Benign according to our data. Variant chr17-76872805-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648321.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MGAT5B	NM_001199172.2 link	c.69-46C>T		intron_variant		ENST00000569840.7	NP_001186101.1	Q3V5L5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MGAT5B	ENST00000569840.7 link	c.69-46C>T		intron_variant		5	NM_001199172.2	ENSP00000456037.2		Q3V5L5-1

Frequencies

GnomAD3 genomes

AF:

0.00425

AC:

647

AN:

152232

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00150

Gnomad AMI

AF:

0.00549

Gnomad AMR

AF:

0.00111

Gnomad ASJ

AF:

0.0256

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00235

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00623

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.00471

AC:

1176

AN:

249816

Hom.:

AF XY:

0.00466

AC XY:

631

AN XY:

135304

show subpopulations

Gnomad AFR exome

AF:

0.00149

Gnomad AMR exome

AF:

0.00281

Gnomad ASJ exome

AF:

0.0237

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00206

Gnomad FIN exome

AF:

0.00214

Gnomad NFE exome

AF:

0.00592

Gnomad OTH exome

AF:

0.00671

GnomAD4 exome

AF:

0.00524

AC:

7661

AN:

1461728

Hom.:

Cov.:

AF XY:

0.00524

AC XY:

3809

AN XY:

727164

show subpopulations

Gnomad4 AFR exome

AF:

0.00158

Gnomad4 AMR exome

AF:

0.00268

Gnomad4 ASJ exome

AF:

0.0233

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00203

Gnomad4 FIN exome

AF:

0.00223

Gnomad4 NFE exome

AF:

0.00554

Gnomad4 OTH exome

AF:

0.00613

GnomAD4 genome

AF:

0.00425

AC:

648

AN:

152350

Hom.:

Cov.:

AF XY:

0.00352

AC XY:

262

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00152

Gnomad4 AMR

AF:

0.00111

Gnomad4 ASJ

AF:

0.0256

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00235

Gnomad4 NFE

AF:

0.00623

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00653

Hom.:

Bravo

AF:

0.00433

TwinsUK

AF:

0.00458

AC:

ALSPAC

AF:

0.00545

AC:

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.00779

AC:

ExAC

AF:

0.00436

AC:

529

EpiCase

AF:

0.00840

EpiControl

AF:

0.00771

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

MGAT5B: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.77

CADD

Benign

2.9

DANN

Benign

0.96

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0073

LIST_S2

Benign

0.43

M_CAP

Uncertain

0.089

MetaRNN

Benign

0.0035

MetaSVM

Benign

-1.0

PROVEAN

Benign

-0.11

REVEL

Benign

0.012

Sift

Uncertain

0.010

Sift4G

Uncertain

0.025

Polyphen

0.0050

Vest4

0.078

MVP

0.076

MPC

0.35

ClinPred

0.0070

GERP RS

-1.5

gMVP

0.28

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over