rs1695

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000852.4(GSTP1):c.313A>G(p.Ile105Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 1,605,938 control chromosomes in the GnomAD database, including 96,157 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 10253 hom., cov: 32)

Exomes 𝑓: 0.34 ( 85904 hom. )

Consequence

GSTP1
NM_000852.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.46

Variant links:

Genes affected

GSTP1 (HGNC:4638): (glutathione S-transferase pi 1) Glutathione S-transferases (GSTs) are a family of enzymes that play an important role in detoxification by catalyzing the conjugation of many hydrophobic and electrophilic compounds with reduced glutathione. Based on their biochemical, immunologic, and structural properties, the soluble GSTs are categorized into 4 main classes: alpha, mu, pi, and theta. This GST family member is a polymorphic gene encoding active, functionally different GSTP1 variant proteins that are thought to function in xenobiotic metabolism and play a role in susceptibility to cancer, and other diseases. [provided by RefSeq, Jul 2008]

GSTP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=4.4708562E-5).

BP6

Variant 11-67585218-A-G is Benign according to our data. Variant chr11-67585218-A-G is described in ClinVar as [Benign]. Clinvar id is 37340.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSTP1	NM_000852.4 link	c.313A>G	p.Ile105Val	missense_variant	Exon 5 of 7	ENST00000398606.10	NP_000843.1	P09211V9HWE9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSTP1	ENST00000398606.10 link	c.313A>G	p.Ile105Val	missense_variant	Exon 5 of 7	1	NM_000852.4	ENSP00000381607.3		P09211

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54588

AN:

151674

Hom.:

10241

Cov.:

show subpopulations

Gnomad AFR

AF:

0.443

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.420

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.263

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.339

Gnomad OTH

AF:

0.350

GnomAD3 exomes

AF:

0.339

AC:

84137

AN:

248500

Hom.:

15539

AF XY:

0.329

AC XY:

44394

AN XY:

134908

show subpopulations

Gnomad AFR exome

AF:

0.448

Gnomad AMR exome

AF:

0.519

Gnomad ASJ exome

AF:

0.213

Gnomad EAS exome

AF:

0.177

Gnomad SAS exome

AF:

0.287

Gnomad FIN exome

AF:

0.271

Gnomad NFE exome

AF:

0.333

Gnomad OTH exome

AF:

0.334

GnomAD4 exome

AF:

0.339

AC:

493382

AN:

1454146

Hom.:

85904

Cov.:

AF XY:

0.336

AC XY:

242988

AN XY:

723844

show subpopulations

Gnomad4 AFR exome

AF:

0.455

Gnomad4 AMR exome

AF:

0.505

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.161

Gnomad4 SAS exome

AF:

0.286

Gnomad4 FIN exome

AF:

0.275

Gnomad4 NFE exome

AF:

0.346

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.360

AC:

54640

AN:

151792

Hom.:

10253

Cov.:

AF XY:

0.354

AC XY:

26226

AN XY:

74184

show subpopulations

Gnomad4 AFR

AF:

0.443

Gnomad4 AMR

AF:

0.420

Gnomad4 ASJ

AF:

0.212

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.268

Gnomad4 FIN

AF:

0.263

Gnomad4 NFE

AF:

0.339

Gnomad4 OTH

AF:

0.347

Alfa

AF:

0.329

Hom.:

20651

Bravo

AF:

0.380

TwinsUK

AF:

0.350

AC:

1296

ALSPAC

AF:

0.345

AC:

1328

ESP6500AA

AF:

0.420

AC:

1749

ESP6500EA

AF:

0.332

AC:

2786

ExAC

AF:

0.332

AC:

40134

Asia WGS

AF:

0.278

AC:

968

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 09, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 25799091, 26663067, 27984487, 25591549, 24582550, 24547706, 23977100, 24919441, 23979883, 24185126, 23552977, 27271084, 10376763, 23278642, 20674822, 17250723, 20091863, 9525277, 20840864, 19383894, 22960333, 23142420, 22525558, 22326267, 18988661, 22206016, 22251241, 9299520, 9281308, 20608166, 23826324, 19027952, 21128213, 20032816, 21993019, 23278115, 9092542, 20041472) -

Abnormality of immune system physiology

Benign:1

Sep 06, 2021

iDNA Genomics

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: reference population

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.87

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.0020

DANN

Benign

0.32

DEOGEN2

Benign

0.053

T;.;T

Eigen

Benign

-2.1

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.0087

LIST_S2

Benign

0.014

.;T;T

MetaRNN

Benign

0.000045

T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-0.095

N;.;N

PrimateAI

Benign

0.27

PROVEAN

Benign

0.29

N;N;.

REVEL

Benign

0.013

Sift

Benign

1.0

T;T;.

Polyphen

0.0

B;.;B

Vest4

0.018

MPC

0.028

ClinPred

0.0015

GERP RS

-1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.4

Varity_R

0.18

gMVP

0.079

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