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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(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

15

Clinical Significance

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

Conservation

PhyloP100: -1.46

Links

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
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
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 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) -
Abnormality of immune system physiology Benign:1
Benign, no assertion criteria providedreference populationiDNA GenomicsSep 06, 2021- -
Neoplasm of the large intestine Other:1
not provided, no assertion 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
0.0030
Dann
Benign
0.32
DEOGEN2
Benign
0.053
T;.;T
Eigen
Benign
-2.1
Eigen_PC
Benign
-2.0
FATHMM_MKL
Benign
0.0087
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

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;