rs4925

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_004832.3(GSTO1):c.419C>A(p.Ala140Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,519,098 control chromosomes in the GnomAD database, including 58,948 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.24 ( 4921 hom., cov: 33)

Exomes 𝑓: 0.27 ( 54027 hom. )

Consequence

GSTO1
NM_004832.3 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.992

Publications

196 publications found

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:

ENSG00000302058 (HGNC:):

ENSG00000302058 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015232861).

BP6

Variant 10-104263031-C-A is Benign according to our data. Variant chr10-104263031-C-A is described in ClinVar as Benign. ClinVar VariationId is 3059603.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
GSTO1	NM_004832.3 link	c.419C>A	p.Ala140Asp	missense_variant	Exon 4 of 6	ENST00000369713.10	NP_004823.1
GSTO1	NM_001191003.2 link	c.335C>A	p.Ala112Asp	missense_variant	Exon 4 of 6		NP_001177932.1
GSTO1	NM_001191002.2 link	c.367-3053C>A		intron_variant	Intron 3 of 4		NP_001177931.1
LOC124902497	XR_007062284.1 link	n.365+5522G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTO1	ENST00000369713.10 link	c.419C>A	p.Ala140Asp	missense_variant	Exon 4 of 6	1	NM_004832.3	ENSP00000358727.5

Frequencies

GnomAD3 genomes

AF:

0.236

AC:

35883

AN:

152060

Hom.:

4920

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.337

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.268

Gnomad MID

AF:

0.347

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.274

GnomAD2 exomes

AF:

0.248

AC:

60720

AN:

245134

AF XY:

0.254

show subpopulations

Gnomad AFR exome

AF:

0.0976

Gnomad AMR exome

AF:

0.178

Gnomad ASJ exome

AF:

0.315

Gnomad EAS exome

AF:

0.135

Gnomad FIN exome

AF:

0.274

Gnomad NFE exome

AF:

0.310

Gnomad OTH exome

AF:

0.282

GnomAD4 exome

AF:

0.272

AC:

372389

AN:

1366918

Hom.:

54027

Cov.:

AF XY:

0.273

AC XY:

186857

AN XY:

684390

show subpopulations

African (AFR)

AF:

0.0884

AC:

2855

AN:

32300

American (AMR)

AF:

0.183

AC:

7923

AN:

43210

Ashkenazi Jewish (ASJ)

AF:

0.317

AC:

7922

AN:

25022

East Asian (EAS)

AF:

0.127

AC:

5009

AN:

39354

South Asian (SAS)

AF:

0.195

AC:

16294

AN:

83466

European-Finnish (FIN)

AF:

0.274

AC:

14549

AN:

53014

Middle Eastern (MID)

AF:

0.317

AC:

1719

AN:

5418

European-Non Finnish (NFE)

AF:

0.293

AC:

301183

AN:

1027848

Other (OTH)

AF:

0.261

AC:

14935

AN:

57286

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.418

Heterozygous variant carriers

10496

20992

31488

41984

52480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9158

18316

27474

36632

45790

<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:

0.236

AC:

35893

AN:

152180

Hom.:

4921

Cov.:

AF XY:

0.233

AC XY:

17319

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.103

AC:

4259

AN:

41540

American (AMR)

AF:

0.236

AC:

3613

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.337

AC:

1169

AN:

3468

East Asian (EAS)

AF:

0.138

AC:

717

AN:

5182

South Asian (SAS)

AF:

0.207

AC:

996

AN:

4820

European-Finnish (FIN)

AF:

0.268

AC:

2832

AN:

10578

Middle Eastern (MID)

AF:

0.346

AC:

101

AN:

292

European-Non Finnish (NFE)

AF:

0.315

AC:

21446

AN:

67988

Other (OTH)

AF:

0.271

AC:

572

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1377

2754

4131

5508

6885

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

370

740

1110

1480

1850

<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:

0.290

Hom.:

34456

Bravo

AF:

0.229

TwinsUK

AF:

0.313

AC:

1162

ALSPAC

AF:

0.314

AC:

1212

ESP6500AA

AF:

0.109

AC:

481

ESP6500EA

AF:

0.310

AC:

2665

ExAC

AF:

0.252

AC:

30562

Asia WGS

AF:

0.161

AC:

561

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

GSTO1-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.022

.;T;T

Eigen

Benign

-0.83

Eigen_PC

Benign

-0.78

FATHMM_MKL

Benign

0.43

LIST_S2

Benign

0.73

T;T;T

MetaRNN

Benign

0.0015

T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.49

.;N;.

PhyloP100

0.99

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.82

N;N;N

REVEL

Benign

0.053

Sift

Uncertain

0.015

D;D;T

Sift4G

Benign

0.44

T;T;T

Polyphen

0.23

.;B;.

Vest4

0.11

MPC

0.24

ClinPred

0.0080

GERP RS

3.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.35

gMVP

0.51

Mutation Taster

=94/6

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over