Variant chr9-133162355-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000372040.9(GBGT1):c.58C>T(p.Leu20Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 1,248,388 control chromosomes in the GnomAD database, including 21,095 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.23 ( 4709 hom., cov: 32)

Exomes 𝑓: 0.11 ( 16386 hom. )

Consequence

GBGT1
ENST00000372040.9 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0200

Variant links:

Genes affected

GBGT1 (HGNC:20460): (globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (FORS blood group)) This gene encodes a glycosyltransferase that plays a role in the synthesis of Forssman glycolipid (FG), a member of the globoseries glycolipid family. Glycolipids such as FG form attachment sites for the binding of pathogens to cells; expression of this protein may determine host tropism to microorganisms. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

GBGT1 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 (MetaRNN=2.3922324E-4).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GBGT1	NM_021996.6 linkuse as main transcript	c.58C>T	p.Leu20Phe	missense_variant	2/7	ENST00000372040.9	NP_068836.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GBGT1	ENST00000372040.9 linkuse as main transcript	c.58C>T	p.Leu20Phe	missense_variant	2/7	1	NM_021996.6	ENSP00000361110	P1	Q8N5D6-1

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

33891

AN:

148106

Hom.:

4702

Cov.:

show subpopulations

Gnomad AFR

AF:

0.255

Gnomad AMI

AF:

0.297

Gnomad AMR

AF:

0.239

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.551

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.201

Gnomad MID

AF:

0.194

Gnomad NFE

AF:

0.188

Gnomad OTH

AF:

0.227

GnomAD3 exomes

AF:

0.114

AC:

19511

AN:

171460

Hom.:

3149

AF XY:

0.106

AC XY:

9737

AN XY:

91570

show subpopulations

Gnomad AFR exome

AF:

0.142

Gnomad AMR exome

AF:

0.115

Gnomad ASJ exome

AF:

0.0411

Gnomad EAS exome

AF:

0.455

Gnomad SAS exome

AF:

0.123

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.0681

Gnomad OTH exome

AF:

0.121

GnomAD4 exome

AF:

0.106

AC:

116128

AN:

1100172

Hom.:

16386

Cov.:

AF XY:

0.114

AC XY:

62925

AN XY:

552954

show subpopulations

Gnomad4 AFR exome

AF:

0.140

Gnomad4 AMR exome

AF:

0.145

Gnomad4 ASJ exome

AF:

0.101

Gnomad4 EAS exome

AF:

0.524

Gnomad4 SAS exome

AF:

0.235

Gnomad4 FIN exome

AF:

0.191

Gnomad4 NFE exome

AF:

0.0686

Gnomad4 OTH exome

AF:

0.136

GnomAD4 genome

AF:

0.229

AC:

33932

AN:

148216

Hom.:

4709

Cov.:

AF XY:

0.235

AC XY:

16969

AN XY:

72236

show subpopulations

Gnomad4 AFR

AF:

0.256

Gnomad4 AMR

AF:

0.239

Gnomad4 ASJ

AF:

0.156

Gnomad4 EAS

AF:

0.549

Gnomad4 SAS

AF:

0.326

Gnomad4 FIN

AF:

0.201

Gnomad4 NFE

AF:

0.188

Gnomad4 OTH

AF:

0.229

Alfa

AF:

0.202

Hom.:

6036

Bravo

AF:

0.240

TwinsUK

AF:

0.190

AC:

706

ALSPAC

AF:

0.193

AC:

742

ESP6500AA

AF:

0.276

AC:

1215

ESP6500EA

AF:

0.192

AC:

1652

ExAC

AF:

0.244

AC:

29576

Asia WGS

AF:

0.311

AC:

909

AN:

2934

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.037

.;T;.;.;.;.;.;.;.;.

Eigen

Benign

-0.77

Eigen_PC

Benign

-0.83

FATHMM_MKL

Benign

0.045

LIST_S2

Benign

0.57

T;T;T;T;T;T;T;.;T;T

MetaRNN

Benign

0.00024

T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

1.4

.;L;L;.;L;.;.;.;.;.

MutationTaster

Benign

1.0

P;P;P;P;P;P

PROVEAN

Benign

-0.21

.;N;N;.;N;.;D;.;N;.

REVEL

Benign

0.036

Sift

Uncertain

0.025

.;D;D;.;D;.;D;.;T;.

Sift4G

Uncertain

0.028

.;D;D;.;T;.;D;.;D;.

Polyphen

0.0020, 0.033

.;B;B;.;.;.;.;.;.;.

Vest4

0.036, 0.072, 0.060, 0.091, 0.099

MPC

0.11

ClinPred

0.0046

GERP RS

0.89

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.069

gMVP

0.48

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