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GeneBe

rs1695

Variant summary

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

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. 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 ( 10253 hom., cov: 32)
Exomes 𝑓: 0.34 ( 85904 hom. )

Consequence

GSTP1
NM_000852.4 missense

Scores

15

Clinical Significance

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

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]

Genome browser will be placed here

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
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/exons MANE UniProt
GSTP1NM_000852.4 linkuse as main transcriptc.313A>G p.Ile105Val missense_variant 5/7 ENST00000398606.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GSTP1ENST00000398606.10 linkuse as main transcriptc.313A>G p.Ile105Val missense_variant 5/71 NM_000852.4 P1

Frequencies

GnomAD3 genomes
AF:
0.360
AC:
54588
AN:
151674
Hom.:
10241
Cov.:
32
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.:
31
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.:
32
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:2Other:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Abnormality of immune system physiology Benign:1
Benign, no assertion criteria providedreference populationiDNA GenomicsSep 06, 2021- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 09, 2021This 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) -
Neoplasm of the large intestine Other:1
not provided, no classification providedliterature onlyDatabase 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
T
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
N
MetaRNN
Benign
0.000045
T;T;T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
-0.095
N;.;N
PrimateAI
Benign
0.27
T
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
T
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.

Other links and lift over

dbSNP: rs1695; hg19: chr11-67352689; COSMIC: COSV66992376; COSMIC: COSV66992376; API