chr6-52902401-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000847.5(GSTA3):c.217A>G(p.Asn73Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0102 in 1,614,006 control chromosomes in the GnomAD database, including 122 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.0077 ( 6 hom., cov: 32)
Exomes 𝑓: 0.010 ( 116 hom. )
Consequence
GSTA3
NM_000847.5 missense
NM_000847.5 missense
Scores
9
7
Clinical Significance
Conservation
PhyloP100: 4.24
Genes affected
GSTA3 (HGNC:4628): (glutathione S-transferase alpha 3) 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 genes that are located in a cluster mapped to chromosome 6. Genes of the alpha class are highly related and encode enzymes with glutathione peroxidase activity. However, during evolution, this alpha class gene diverged accumulating mutations in the active site that resulted in differences in substrate specificity and catalytic activity. The enzyme encoded by this gene catalyzes the double bond isomerization of precursors for progesterone and testosterone during the biosynthesis of steroid hormones. An additional transcript variant has been identified, but its full length sequence has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.012420088).
BP6
?
Variant 6-52902401-T-C is Benign according to our data. Variant chr6-52902401-T-C is described in ClinVar as [Benign]. Clinvar id is 774447.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTA3 | NM_000847.5 | c.217A>G | p.Asn73Asp | missense_variant | 4/7 | ENST00000211122.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTA3 | ENST00000211122.4 | c.217A>G | p.Asn73Asp | missense_variant | 4/7 | 1 | NM_000847.5 | P1 | |
GSTA3 | ENST00000370968.5 | c.67A>G | p.Asn23Asp | missense_variant | 3/6 | 1 | |||
GSTA3 | ENST00000431899.2 | c.67A>G | p.Asn23Asp | missense_variant | 2/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00770 AC: 1172AN: 152186Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00799 AC: 2010AN: 251432Hom.: 18 AF XY: 0.00823 AC XY: 1119AN XY: 135884
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GnomAD4 exome AF: 0.0104 AC: 15254AN: 1461702Hom.: 116 Cov.: 31 AF XY: 0.0103 AC XY: 7481AN XY: 727148
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GnomAD4 genome ? AF: 0.00770 AC: 1172AN: 152304Hom.: 6 Cov.: 32 AF XY: 0.00755 AC XY: 562AN XY: 74460
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 19, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;T;.
Polyphen
0.99
.;D;.
Vest4
MVP
MPC
0.19
ClinPred
T
GERP RS
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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