rs1695

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000852(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 0.36 in 151674 control chromosomes in the gnomAD Genomes database, including 10241 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.36 ( 10241 hom., cov: 32)

Exomes 𝑓: 0.34 ( 15539 hom. )

Consequence

GSTP1
NM_000852 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:2O:1

Conservation

PhyloP100: -1.46

Links

GSTP1 (HGNC:4638):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 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_single_submitter, 1 stars.

BA1

GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSTP1	NM_000852.4 linkuse as main transcript	c.313A>G	p.Ile105Val	missense_variant	5/7	ENST00000398606.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSTP1	ENST00000398606.10 linkuse as main transcript	c.313A>G	p.Ile105Val	missense_variant	5/7	1	NM_000852.4	P1

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

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

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:2Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 09, 2021

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

Benign, no assertion criteria provided

reference population

iDNA Genomics

Sep 06, 2021

- -

Neoplasm of the large intestine

Other:1

not provided, no assertion provided

literature only

Database of Curated Mutations (DoCM)

Mar 10, 2016

- -

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

0.0030

Dann

Benign

0.32

DEOGEN2

Benign

0.053

T;.;T

Eigen

Benign

-2.1

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.0087

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

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over