rs34400162
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_183239.2(GSTO2):c.121G>A(p.Val41Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000442 in 1,613,956 control chromosomes in the GnomAD database, including 5 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_183239.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTO2 | NM_183239.2 | c.121G>A | p.Val41Ile | missense_variant | 3/7 | ENST00000338595.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTO2 | ENST00000338595.7 | c.121G>A | p.Val41Ile | missense_variant | 3/7 | 1 | NM_183239.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00170 AC: 259AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000561 AC: 141AN: 251280Hom.: 0 AF XY: 0.000412 AC XY: 56AN XY: 135840
GnomAD4 exome AF: 0.000311 AC: 454AN: 1461736Hom.: 5 Cov.: 31 AF XY: 0.000323 AC XY: 235AN XY: 727194
GnomAD4 genome AF: 0.00171 AC: 260AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.00152 AC XY: 113AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at