Variant chr9-133154258-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_021996.6(GBGT1):c.363C>A(p.Tyr121Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0647 in 1,519,242 control chromosomes in the GnomAD database, including 3,502 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 0.060 ( 323 hom., cov: 32)

Exomes 𝑓: 0.065 ( 3179 hom. )

Consequence

GBGT1
NM_021996.6 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.733

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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GBGT1	NM_021996.6 linkuse as main transcript	c.363C>A	p.Tyr121Ter	stop_gained	7/7	ENST00000372040.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GBGT1	ENST00000372040.9 linkuse as main transcript	c.363C>A	p.Tyr121Ter	stop_gained	7/7	1	NM_021996.6	P1	Q8N5D6-1

Frequencies

GnomAD3 genomes

AF:

0.0598

AC:

9100

AN:

152138

Hom.:

320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0409

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.0432

Gnomad ASJ

AF:

0.0813

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0548

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0722

Gnomad OTH

AF:

0.0650

GnomAD3 exomes

AF:

0.0578

AC:

10722

AN:

185574

Hom.:

406

AF XY:

0.0598

AC XY:

5883

AN XY:

98446

show subpopulations

Gnomad AFR exome

AF:

0.0412

Gnomad AMR exome

AF:

0.0334

Gnomad ASJ exome

AF:

0.0872

Gnomad EAS exome

AF:

0.000180

Gnomad SAS exome

AF:

0.0481

Gnomad FIN exome

AF:

0.105

Gnomad NFE exome

AF:

0.0706

Gnomad OTH exome

AF:

0.0621

GnomAD4 exome

AF:

0.0653

AC:

89199

AN:

1366986

Hom.:

3179

Cov.:

AF XY:

0.0657

AC XY:

43960

AN XY:

669032

show subpopulations

Gnomad4 AFR exome

AF:

0.0432

Gnomad4 AMR exome

AF:

0.0336

Gnomad4 ASJ exome

AF:

0.0856

Gnomad4 EAS exome

AF:

0.000181

Gnomad4 SAS exome

AF:

0.0551

Gnomad4 FIN exome

AF:

0.100

Gnomad4 NFE exome

AF:

0.0681

Gnomad4 OTH exome

AF:

0.0603

GnomAD4 genome

AF:

0.0598

AC:

9106

AN:

152256

Hom.:

323

Cov.:

AF XY:

0.0605

AC XY:

4501

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0409

Gnomad4 AMR

AF:

0.0431

Gnomad4 ASJ

AF:

0.0813

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.0559

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.0722

Gnomad4 OTH

AF:

0.0639

Alfa

AF:

0.0672

Hom.:

728

Bravo

AF:

0.0538

TwinsUK

AF:

0.0628

AC:

233

ALSPAC

AF:

0.0669

AC:

258

ESP6500AA

AF:

0.0452

AC:

199

ESP6500EA

AF:

0.0731

AC:

629

ExAC

AF:

0.0572

AC:

6693

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.37

CADD

Pathogenic

DANN

Uncertain

0.99

Eigen

Uncertain

0.34

Eigen_PC

Benign

0.11

FATHMM_MKL

Benign

0.72

LIST_S2

Benign

0.26

T;T

MetaRNN

Benign

0.0018

T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

D;D;D;N;D

PROVEAN

Benign

0.62

.;N

REVEL

Benign

0.015

Sift

Benign

0.60

.;T

Vest4

0.38

ClinPred

0.094

GERP RS

1.5

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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