chr10-104263054-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_004832.3(GSTO1):āc.442A>Gā(p.Lys148Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000149 in 1,342,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004832.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTO1 | NM_004832.3 | c.442A>G | p.Lys148Glu | missense_variant | 4/6 | ENST00000369713.10 | |
LOC124902497 | XR_007062284.1 | n.365+5499T>C | intron_variant, non_coding_transcript_variant | ||||
GSTO1 | NM_001191003.2 | c.358A>G | p.Lys120Glu | missense_variant | 4/6 | ||
GSTO1 | NM_001191002.2 | c.367-3030A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTO1 | ENST00000369713.10 | c.442A>G | p.Lys148Glu | missense_variant | 4/6 | 1 | NM_004832.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000815 AC: 2AN: 245388Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132668
GnomAD4 exome AF: 0.00000149 AC: 2AN: 1342738Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 674142
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2023 | The c.442A>G (p.K148E) alteration is located in exon 4 (coding exon 4) of the GSTO1 gene. This alteration results from a A to G substitution at nucleotide position 442, causing the lysine (K) at amino acid position 148 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at