chr10-104266106-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_004832.3(GSTO1):c.488C>T(p.Thr163Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00306 in 1,600,274 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004832.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTO1 | NM_004832.3 | c.488C>T | p.Thr163Ile | missense_variant | 5/6 | ENST00000369713.10 | |
LOC124902497 | XR_007062284.1 | n.365+2447G>A | intron_variant, non_coding_transcript_variant | ||||
GSTO1 | NM_001191003.2 | c.404C>T | p.Thr135Ile | missense_variant | 5/6 | ||
GSTO1 | NM_001191002.2 | c.389C>T | p.Thr130Ile | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTO1 | ENST00000369713.10 | c.488C>T | p.Thr163Ile | missense_variant | 5/6 | 1 | NM_004832.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00166 AC: 252AN: 152178Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00201 AC: 504AN: 251360Hom.: 0 AF XY: 0.00189 AC XY: 257AN XY: 135840
GnomAD4 exome AF: 0.00320 AC: 4638AN: 1447978Hom.: 11 Cov.: 26 AF XY: 0.00304 AC XY: 2194AN XY: 721220
GnomAD4 genome ? AF: 0.00165 AC: 252AN: 152296Hom.: 1 Cov.: 33 AF XY: 0.00161 AC XY: 120AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at