chr11-67586108-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000852.4(GSTP1):c.341C>T(p.Ala114Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 1,608,182 control chromosomes in the GnomAD database, including 5,074 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.055 ( 310 hom., cov: 31)
Exomes 𝑓: 0.076 ( 4764 hom. )
Consequence
GSTP1
NM_000852.4 missense
NM_000852.4 missense
Scores
2
13
Clinical Significance
Conservation
PhyloP100: 0.0320
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0015839636).
BP6
?
Variant 11-67586108-C-T is Benign according to our data. Variant chr11-67586108-C-T is described in ClinVar as [Benign]. Clinvar id is 1264275.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0826 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTP1 | NM_000852.4 | c.341C>T | p.Ala114Val | missense_variant | 6/7 | ENST00000398606.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTP1 | ENST00000398606.10 | c.341C>T | p.Ala114Val | missense_variant | 6/7 | 1 | NM_000852.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0548 AC: 8315AN: 151818Hom.: 311 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0593 AC: 14726AN: 248494Hom.: 565 AF XY: 0.0618 AC XY: 8333AN XY: 134870
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GnomAD4 exome AF: 0.0763 AC: 111118AN: 1456246Hom.: 4764 Cov.: 30 AF XY: 0.0764 AC XY: 55344AN XY: 724640
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GnomAD4 genome ? AF: 0.0547 AC: 8310AN: 151936Hom.: 310 Cov.: 31 AF XY: 0.0538 AC XY: 3995AN XY: 74254
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293
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308
ESP6500AA
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64
ESP6500EA
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690
ExAC
?
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7205
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other: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: 10780269, 23142420, 23437223, 9299520, 9092542) - |
Pulmonary disease, chronic obstructive, susceptibility to Other:1
association, no assertion criteria provided | research | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | Jul 05, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
PrimateAI
Benign
T
PROVEAN
Benign
N;.;.
REVEL
Benign
Sift
Benign
T;.;.
Polyphen
P;P;.
Vest4
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at