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
NM_000852 missense
Scores
15
Clinical Significance
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 |
---|---|---|---|---|---|---|---|
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
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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 AF XY: 0.336 AC XY: 242988AN XY: 723844
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ALSPAC
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1328
ESP6500AA
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40134
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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 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) - |
Abnormality of immune system physiology Benign:1
Benign, no assertion criteria provided | reference population | iDNA Genomics | Sep 06, 2021 | - - |
Neoplasm of the large intestine Other:1
not provided, no assertion 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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at