Genetic Variant GSTO2:c.366+20T>C (chr10-104278136-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_183239.2(GSTO2):c.366+20T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 1,581,530 control chromosomes in the GnomAD database, including 171,336 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 0.53 ( 23017 hom., cov: 33)

Exomes 𝑓: 0.45 ( 148319 hom. )

Consequence

GSTO2
NM_183239.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

22 publications found

Variant links:

Genes affected

GSTO2 (HGNC:23064): (glutathione S-transferase omega 2) The protein encoded by this gene is an omega class glutathione S-transferase (GST). GSTs are involved in the metabolism of xenobiotics and carcinogens. Four transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2010]

GSTO2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTO2	NM_183239.2 link	c.366+20T>C		intron_variant	Intron 4 of 6	ENST00000338595.7	NP_899062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTO2	ENST00000338595.7 link	c.366+20T>C		intron_variant	Intron 4 of 6	1	NM_183239.2	ENSP00000345023.1

Frequencies

GnomAD3 genomes

AF:

0.528

AC:

80258

AN:

151980

Hom.:

22971

Cov.:

show subpopulations

Gnomad AFR

AF:

0.764

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.412

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.480

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.527

GnomAD2 exomes

AF:

0.449

AC:

109286

AN:

243144

AF XY:

0.452

show subpopulations

Gnomad AFR exome

AF:

0.769

Gnomad AMR exome

AF:

0.293

Gnomad ASJ exome

AF:

0.512

Gnomad EAS exome

AF:

0.402

Gnomad FIN exome

AF:

0.398

Gnomad NFE exome

AF:

0.453

Gnomad OTH exome

AF:

0.465

GnomAD4 exome

AF:

0.451

AC:

644448

AN:

1429430

Hom.:

148319

Cov.:

AF XY:

0.452

AC XY:

321961

AN XY:

712390

show subpopulations

African (AFR)

AF:

0.775

AC:

25501

AN:

32908

American (AMR)

AF:

0.304

AC:

13388

AN:

44070

Ashkenazi Jewish (ASJ)

AF:

0.519

AC:

13436

AN:

25896

East Asian (EAS)

AF:

0.386

AC:

15234

AN:

39464

South Asian (SAS)

AF:

0.486

AC:

41379

AN:

85128

European-Finnish (FIN)

AF:

0.397

AC:

21110

AN:

53130

Middle Eastern (MID)

AF:

0.546

AC:

2587

AN:

4736

European-Non Finnish (NFE)

AF:

0.446

AC:

484026

AN:

1084938

Other (OTH)

AF:

0.470

AC:

27787

AN:

59160

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

17578

35155

52733

70310

87888

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14564

29128

43692

58256

72820

<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:

0.528

AC:

80354

AN:

152100

Hom.:

23017

Cov.:

AF XY:

0.522

AC XY:

38827

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.764

AC:

31726

AN:

41514

American (AMR)

AF:

0.411

AC:

6286

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.517

AC:

1794

AN:

3470

East Asian (EAS)

AF:

0.410

AC:

2121

AN:

5174

South Asian (SAS)

AF:

0.480

AC:

2315

AN:

4822

European-Finnish (FIN)

AF:

0.381

AC:

4026

AN:

10564

Middle Eastern (MID)

AF:

0.605

AC:

178

AN:

294

European-Non Finnish (NFE)

AF:

0.448

AC:

30417

AN:

67944

Other (OTH)

AF:

0.525

AC:

1109

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1790

3580

5369

7159

8949

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

688

1376

2064

2752

3440

<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:

0.497

Hom.:

33305

Bravo

AF:

0.540

Asia WGS

AF:

0.473

AC:

1641

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.40

(source)

DANN

Benign

0.47

PhyloP100

-1.5

Mutation Taster

=100/0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over