chr10-104255250-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004832.3(GSTO1):āc.122T>Cā(p.Val41Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,611,956 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000033 ( 0 hom., cov: 32)
Exomes š: 0.000010 ( 0 hom. )
Consequence
GSTO1
NM_004832.3 missense
NM_004832.3 missense
Scores
1
8
10
Clinical Significance
Conservation
PhyloP100: 5.72
Genes affected
GSTO1 (HGNC:13312): (glutathione S-transferase omega 1) The protein encoded by this gene is an omega class glutathione S-transferase (GST) with glutathione-dependent thiol transferase and dehydroascorbate reductase activities. GSTs are involved in the metabolism of xenobiotics and carcinogens. The encoded protein acts as a homodimer and is found in the cytoplasm. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTO1 | NM_004832.3 | c.122T>C | p.Val41Ala | missense_variant | 2/6 | ENST00000369713.10 | |
LOC124902497 | XR_007062284.1 | n.366-6658A>G | intron_variant, non_coding_transcript_variant | ||||
GSTO1 | NM_001191003.2 | c.38T>C | p.Val13Ala | missense_variant | 2/6 | ||
GSTO1 | NM_001191002.2 | c.122T>C | p.Val41Ala | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTO1 | ENST00000369713.10 | c.122T>C | p.Val41Ala | missense_variant | 2/6 | 1 | NM_004832.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152076Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250984Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135780
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GnomAD4 exome AF: 0.0000103 AC: 15AN: 1459762Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726328
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74408
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.122T>C (p.V41A) alteration is located in exon 2 (coding exon 2) of the GSTO1 gene. This alteration results from a T to C substitution at nucleotide position 122, causing the valine (V) at amino acid position 41 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;.;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T;T;T
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;N;N;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;T;D;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
0.99
.;.;D;.;.
Vest4
MutPred
0.83
.;Loss of stability (P = 0.0653);Loss of stability (P = 0.0653);.;.;
MVP
MPC
0.55
ClinPred
D
GERP RS
Varity_R
gMVP
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