rs8191445
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000852.4(GSTP1):c.37+34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0324 in 1,557,038 control chromosomes in the GnomAD database, including 1,027 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.026 ( 72 hom., cov: 32)
Exomes 𝑓: 0.033 ( 955 hom. )
Consequence
GSTP1
NM_000852.4 intron
NM_000852.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.283
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0258 (3925/152078) while in subpopulation NFE AF= 0.0379 (2573/67920). AF 95% confidence interval is 0.0367. There are 72 homozygotes in gnomad4. There are 1945 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 72 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GSTP1 | NM_000852.4 | c.37+34G>A | intron_variant | ENST00000398606.10 | NP_000843.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GSTP1 | ENST00000398606.10 | c.37+34G>A | intron_variant | 1 | NM_000852.4 | ENSP00000381607.3 |
Frequencies
GnomAD3 genomes AF: 0.0258 AC: 3927AN: 151964Hom.: 72 Cov.: 32
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GnomAD3 exomes AF: 0.0278 AC: 6716AN: 241730Hom.: 163 AF XY: 0.0278 AC XY: 3677AN XY: 132156
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GnomAD4 exome AF: 0.0332 AC: 46581AN: 1404960Hom.: 955 Cov.: 26 AF XY: 0.0327 AC XY: 22968AN XY: 701734
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GnomAD4 genome AF: 0.0258 AC: 3925AN: 152078Hom.: 72 Cov.: 32 AF XY: 0.0262 AC XY: 1945AN XY: 74362
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at