Variant 10-104263071-AGAG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_004832.3(GSTO1):c.464_465+1delAGG(p.Glu155fs) variant causes a frameshift, splice donor, splice region, intron change. The variant allele was found at a frequency of 0.0305 in 1,302,596 control chromosomes in the GnomAD database, including 1,111 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.029 ( 96 hom., cov: 32)

Exomes 𝑓: 0.031 ( 1015 hom. )

Consequence

GSTO1
NM_004832.3 frameshift, splice_donor, splice_region, intron

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 5.24

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:

GSTO1 (HGNC:):

GSTO1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 10-104263071-AGAG-A is Benign according to our data. Variant chr10-104263071-AGAG-A is described in ClinVar as [Likely_benign]. Clinvar id is 3055930.Status of the report is no_assertion_criteria_provided, 0 stars.

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.464_465+1delAGG	p.Glu155fs	frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant	4/6	ENST00000369713.10	NP_004823.1	P78417-1V9HWG9
GSTO1	NM_001191003.2 linkuse as main transcript	c.380_381+1delAGG	p.Glu127fs	frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant	4/6		NP_001177932.1	P78417-3
GSTO1	NM_001191002.2 linkuse as main transcript	c.367-3008_367-3006delAGG		intron_variant			NP_001177931.1	P78417-2
LOC124902497	XR_007062284.1 linkuse as main transcript	n.365+5479_365+5481delCTC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSTO1	ENST00000369713.10 linkuse as main transcript	c.464_465+1delAGG	p.Glu155fs	frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant	4/6	1	NM_004832.3	ENSP00000358727.5		P78417-1

Frequencies

GnomAD3 genomes

AF:

0.0290

AC:

4419

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0248

Gnomad AMI

AF:

0.00220

Gnomad AMR

AF:

0.0275

Gnomad ASJ

AF:

0.0597

Gnomad EAS

AF:

0.00906

Gnomad SAS

AF:

0.109

Gnomad FIN

AF:

0.00857

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0296

Gnomad OTH

AF:

0.0306

GnomAD3 exomes

AF:

0.0357

AC:

8506

AN:

238046

Hom.:

306

AF XY:

0.0396

AC XY:

5106

AN XY:

128868

show subpopulations

Gnomad AFR exome

AF:

0.0245

Gnomad AMR exome

AF:

0.0151

Gnomad ASJ exome

AF:

0.0639

Gnomad EAS exome

AF:

0.0116

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.00793

Gnomad NFE exome

AF:

0.0305

Gnomad OTH exome

AF:

0.0352

GnomAD4 exome

AF:

0.0307

AC:

35327

AN:

1150270

Hom.:

1015

AF XY:

0.0338

AC XY:

19780

AN XY:

585726

show subpopulations

Gnomad4 AFR exome

AF:

0.0228

Gnomad4 AMR exome

AF:

0.0156

Gnomad4 ASJ exome

AF:

0.0629

Gnomad4 EAS exome

AF:

0.00911

Gnomad4 SAS exome

AF:

0.107

Gnomad4 FIN exome

AF:

0.00991

Gnomad4 NFE exome

AF:

0.0258

Gnomad4 OTH exome

AF:

0.0336

GnomAD4 genome

AF:

0.0291

AC:

4428

AN:

152326

Hom.:

Cov.:

AF XY:

0.0290

AC XY:

2160

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0249

Gnomad4 AMR

AF:

0.0274

Gnomad4 ASJ

AF:

0.0597

Gnomad4 EAS

AF:

0.00908

Gnomad4 SAS

AF:

0.109

Gnomad4 FIN

AF:

0.00857

Gnomad4 NFE

AF:

0.0297

Gnomad4 OTH

AF:

0.0302

Alfa

AF:

0.00979

Hom.:

Bravo

AF:

0.0283

Asia WGS

AF:

0.0600

AC:

209

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

GSTO1-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 31, 2023

This variant is classified as likely 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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over