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GeneBe

rs1138272

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong

The NM_000852.4(GSTP1):c.341C>G(p.Ala114Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A114V) has been classified as Benign.

Frequency

Genomes: not found (cov: 31)

Consequence

GSTP1
NM_000852.4 missense

Scores

16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0320

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 31.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.048787594).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GSTP1NM_000852.4 linkuse as main transcriptc.341C>G p.Ala114Gly missense_variant 6/7 ENST00000398606.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GSTP1ENST00000398606.10 linkuse as main transcriptc.341C>G p.Ala114Gly missense_variant 6/71 NM_000852.4 P1

Frequencies

GnomAD3 genomes
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.32
T
BayesDel_noAF
Benign
-0.70
Cadd
Benign
21
Dann
Benign
0.90
DEOGEN2
Benign
0.096
T;T;T
Eigen
Benign
-0.88
Eigen_PC
Benign
-0.89
FATHMM_MKL
Benign
0.16
N
M_CAP
Benign
0.0046
T
MetaRNN
Benign
0.049
T;T;T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
1.6
L;L;.
PrimateAI
Benign
0.37
T
PROVEAN
Benign
-1.3
N;.;.
REVEL
Benign
0.020
Sift
Benign
0.34
T;.;.
Polyphen
0.0
B;B;.
Vest4
0.26
MutPred
0.35
Loss of catalytic residue at A114 (P = 0.0132);Loss of catalytic residue at A114 (P = 0.0132);.;
MVP
0.42
MPC
0.031
ClinPred
0.031
T
GERP RS
0.53
Varity_R
0.31
gMVP
0.079

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1138272; hg19: chr11-67353579; API