rs3734431
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001512.4(GSTA4):c.547-39T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0762 in 1,538,188 control chromosomes in the GnomAD database, including 4,625 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 0.077 ( 458 hom., cov: 32)
Exomes 𝑓: 0.076 ( 4167 hom. )
Consequence
GSTA4
NM_001512.4 intron
NM_001512.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00400
Genes affected
GSTA4 (HGNC:4629): (glutathione S-transferase alpha 4) Cytosolic and membrane-bound forms of glutathione S-transferase are encoded by two distinct supergene families. These enzymes are involved in cellular defense against toxic, carcinogenic, and pharmacologically active electrophilic compounds. At present, eight distinct classes of the soluble cytoplasmic mammalian glutathione S-transferases have been identified: alpha, kappa, mu, omega, pi, sigma, theta and zeta. This gene encodes a glutathione S-tranferase belonging to the alpha class. The alpha class genes, which are located in a cluster on chromosome 6, are highly related and encode enzymes with glutathione peroxidase activity that function in the detoxification of lipid peroxidation products. Reactive electrophiles produced by oxidative metabolism have been linked to a number of degenerative diseases including Parkinson's disease, Alzheimer's disease, cataract formation, and atherosclerosis. [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=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0845 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTA4 | NM_001512.4 | c.547-39T>C | intron_variant | ENST00000370963.9 | |||
GSTA4 | XM_005249035.5 | c.547-39T>C | intron_variant | ||||
GSTA4 | XM_011514534.4 | c.436-39T>C | intron_variant | ||||
GSTA4 | XM_011514535.4 | c.436-39T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTA4 | ENST00000370963.9 | c.547-39T>C | intron_variant | 1 | NM_001512.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0766 AC: 11650AN: 152124Hom.: 457 Cov.: 32
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GnomAD3 exomes AF: 0.0778 AC: 17738AN: 227940Hom.: 758 AF XY: 0.0790 AC XY: 9751AN XY: 123500
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GnomAD4 exome AF: 0.0761 AC: 105486AN: 1385946Hom.: 4167 Cov.: 22 AF XY: 0.0766 AC XY: 53016AN XY: 692150
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GnomAD4 genome AF: 0.0766 AC: 11660AN: 152242Hom.: 458 Cov.: 32 AF XY: 0.0764 AC XY: 5691AN XY: 74446
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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