Variant rs11509438 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_004832.3(GSTO1):c.622G>A(p.Glu208Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0338 in 1,613,266 control chromosomes in the GnomAD database, including 1,393 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 0.029 ( 96 hom., cov: 32)

Exomes 𝑓: 0.034 ( 1297 hom. )

Consequence

GSTO1
NM_004832.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.53

Variant links:

Genes affected

GSTO1 (HGNC:13312): (glutathione S-transferase omega 1) The protein encoded by this gene is an omega class glutathione S-transferase (GST) with glutathione-dependent thiol transferase and dehydroascorbate reductase activities. GSTs are involved in the metabolism of xenobiotics and carcinogens. The encoded protein acts as a homodimer and is found in the cytoplasm. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

GSTO1 links:

LOC124902497 (HGNC:):

LOC124902497 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=0.0012832582).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSTO1	NM_004832.3 linkuse as main transcript	c.622G>A	p.Glu208Lys	missense_variant	6/6	ENST00000369713.10	NP_004823.1	P78417-1V9HWG9
GSTO1	NM_001191003.2 linkuse as main transcript	c.538G>A	p.Glu180Lys	missense_variant	6/6		NP_001177932.1	P78417-3
GSTO1	NM_001191002.2 linkuse as main transcript	c.523G>A	p.Glu175Lys	missense_variant	5/5		NP_001177931.1	P78417-2
LOC124902497	XR_007062284.1 linkuse as main transcript	n.365+1252C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTO1	ENST00000369713.10 linkuse as main transcript	c.622G>A	p.Glu208Lys	missense_variant	6/6	1	NM_004832.3	ENSP00000358727.5		P78417-1

Frequencies

GnomAD3 genomes

AF:

0.0291

AC:

4424

AN:

152114

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0249

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0275

Gnomad ASJ

AF:

0.0594

Gnomad EAS

AF:

0.00906

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.00868

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0297

Gnomad OTH

AF:

0.0301

GnomAD3 exomes

AF:

0.0368

AC:

9249

AN:

251192

Hom.:

339

AF XY:

0.0412

AC XY:

5596

AN XY:

135784

show subpopulations

Gnomad AFR exome

AF:

0.0249

Gnomad AMR exome

AF:

0.0149

Gnomad ASJ exome

AF:

0.0641

Gnomad EAS exome

AF:

0.0116

Gnomad SAS exome

AF:

0.116

Gnomad FIN exome

AF:

0.00799

Gnomad NFE exome

AF:

0.0311

Gnomad OTH exome

AF:

0.0363

GnomAD4 exome

AF:

0.0342

AC:

50019

AN:

1461034

Hom.:

1297

Cov.:

AF XY:

0.0367

AC XY:

26681

AN XY:

726900

show subpopulations

Gnomad4 AFR exome

AF:

0.0258

Gnomad4 AMR exome

AF:

0.0153

Gnomad4 ASJ exome

AF:

0.0645

Gnomad4 EAS exome

AF:

0.00940

Gnomad4 SAS exome

AF:

0.112

Gnomad4 FIN exome

AF:

0.0100

Gnomad4 NFE exome

AF:

0.0304

Gnomad4 OTH exome

AF:

0.0371

GnomAD4 genome

AF:

0.0291

AC:

4435

AN:

152232

Hom.:

Cov.:

AF XY:

0.0291

AC XY:

2164

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.0250

Gnomad4 AMR

AF:

0.0275

Gnomad4 ASJ

AF:

0.0594

Gnomad4 EAS

AF:

0.00908

Gnomad4 SAS

AF:

0.110

Gnomad4 FIN

AF:

0.00868

Gnomad4 NFE

AF:

0.0297

Gnomad4 OTH

AF:

0.0298

Alfa

AF:

0.0313

Hom.:

132

Bravo

AF:

0.0283

TwinsUK

AF:

0.0302

AC:

112

ALSPAC

AF:

0.0332

AC:

128

ESP6500AA

AF:

0.0288

AC:

127

ESP6500EA

AF:

0.0299

AC:

257

ExAC

AF:

0.0377

AC:

4581

Asia WGS

AF:

0.0600

AC:

210

AN:

3478

EpiCase

AF:

0.0314

EpiControl

AF:

0.0345

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.57

CADD

Benign

0.19

DANN

Benign

0.76

DEOGEN2

Benign

0.040

.;.;T;T;T

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.011

LIST_S2

Benign

0.18

T;T;T;T;T

MetaRNN

Benign

0.0013

T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.15

.;.;N;.;.

PrimateAI

Benign

0.21

PROVEAN

Benign

-0.030

N;N;N;N;N

REVEL

Benign

0.093

Sift

Benign

0.52

T;T;T;T;T

Sift4G

Benign

0.41

T;T;T;T;T

Polyphen

0.0020

.;.;B;.;.

Vest4

0.078

MPC

0.18

ClinPred

0.0013

GERP RS

-7.5

Varity_R

0.18

gMVP

0.32

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