rs11509435
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_004832.3(GSTO1):c.34+49_34+51del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,574,656 control chromosomes in the GnomAD database, including 61,750 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.23 ( 4467 hom., cov: 26)
Exomes 𝑓: 0.28 ( 57283 hom. )
Consequence
GSTO1
NM_004832.3 intron
NM_004832.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.391
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 Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTO1 | NM_004832.3 | c.34+49_34+51del | intron_variant | ENST00000369713.10 | |||
LOC124902497 | XR_007062284.1 | n.366-6417_366-6415del | intron_variant, non_coding_transcript_variant | ||||
GSTO1 | NM_001191002.2 | c.34+49_34+51del | intron_variant | ||||
GSTO1 | NM_001191003.2 | c.-50-152_-50-150del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTO1 | ENST00000369713.10 | c.34+49_34+51del | intron_variant | 1 | NM_004832.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.227 AC: 34415AN: 151836Hom.: 4466 Cov.: 26
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GnomAD3 exomes AF: 0.241 AC: 49221AN: 204394Hom.: 6441 AF XY: 0.246 AC XY: 27386AN XY: 111416
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GnomAD4 exome AF: 0.277 AC: 394252AN: 1422702Hom.: 57283 AF XY: 0.276 AC XY: 195177AN XY: 706724
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GnomAD4 genome ? AF: 0.227 AC: 34425AN: 151954Hom.: 4467 Cov.: 26 AF XY: 0.223 AC XY: 16593AN XY: 74256
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ClinVar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at