chr11-67585218-A-G
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. 13/19 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
NM_000852.4 missense
Scores
15
Clinical Significance
Conservation
PhyloP100: -1.46
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=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 |
---|---|---|---|---|---|---|---|
GSTP1 | NM_000852.4 | 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 | c.313A>G | p.Ile105Val | missense_variant | 5/7 | 1 | NM_000852.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.360 AC: 54588AN: 151674Hom.: 10241 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.339 AC: 84137AN: 248500Hom.: 15539 AF XY: 0.329 AC XY: 44394AN XY: 134908
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GnomAD4 exome AF: 0.339 AC: 493382AN: 1454146Hom.: 85904 Cov.: 31 AF XY: 0.336 AC XY: 242988AN XY: 723844
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GnomAD4 genome ? AF: 0.360 AC: 54640AN: 151792Hom.: 10253 Cov.: 32 AF XY: 0.354 AC XY: 26226AN XY: 74184
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1296
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1328
ESP6500AA
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1749
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2786
ExAC
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40134
Asia WGS
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968
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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 provided | reference population | iDNA Genomics | Sep 06, 2021 | - - |
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) - |
Neoplasm of the large intestine Other:1
not provided, no classification provided | literature only | Database of Curated Mutations (DoCM) | Mar 10, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;.
REVEL
Benign
Sift
Benign
T;T;.
Polyphen
B;.;B
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