rs4986947
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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.414+32C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0581 in 1,583,256 control chromosomes in the GnomAD database, including 3,049 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 0.046 ( 228 hom., cov: 32)
Exomes 𝑓: 0.059 ( 2821 hom. )
Consequence
GSTA4
NM_001512.4 intron
NM_001512.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.857
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=-0.91).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTA4 | NM_001512.4 | c.414+32C>T | intron_variant | ENST00000370963.9 | |||
GSTA4 | XM_005249035.5 | c.414+32C>T | intron_variant | ||||
GSTA4 | XM_011514534.4 | c.303+32C>T | intron_variant | ||||
GSTA4 | XM_011514535.4 | c.303+32C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTA4 | ENST00000370963.9 | c.414+32C>T | intron_variant | 1 | NM_001512.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0464 AC: 7062AN: 152168Hom.: 228 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0482 AC: 11142AN: 231044Hom.: 330 AF XY: 0.0496 AC XY: 6217AN XY: 125418
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GnomAD4 exome AF: 0.0593 AC: 84897AN: 1430970Hom.: 2821 Cov.: 30 AF XY: 0.0588 AC XY: 41866AN XY: 712072
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GnomAD4 genome ? AF: 0.0464 AC: 7059AN: 152286Hom.: 228 Cov.: 32 AF XY: 0.0447 AC XY: 3332AN XY: 74478
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at