NM_145870.3:c.245T>C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_145870.3(GSTZ1):c.245T>C(p.Met82Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 1,613,244 control chromosomes in the GnomAD database, including 523,055 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_145870.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GSTZ1 | NM_145870.3 | c.245T>C | p.Met82Thr | missense_variant | Exon 5 of 9 | ENST00000216465.10 | NP_665877.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GSTZ1 | ENST00000216465.10 | c.245T>C | p.Met82Thr | missense_variant | Exon 5 of 9 | 1 | NM_145870.3 | ENSP00000216465.5 |
Frequencies
GnomAD3 genomes AF: 0.833 AC: 126469AN: 151892Hom.: 52937 Cov.: 30
GnomAD3 exomes AF: 0.813 AC: 204080AN: 251120Hom.: 83442 AF XY: 0.810 AC XY: 110014AN XY: 135744
GnomAD4 exome AF: 0.801 AC: 1170336AN: 1461234Hom.: 470074 Cov.: 44 AF XY: 0.801 AC XY: 582033AN XY: 726960
GnomAD4 genome AF: 0.833 AC: 126569AN: 152010Hom.: 52981 Cov.: 30 AF XY: 0.834 AC XY: 61994AN XY: 74292
ClinVar
Submissions by phenotype
GSTZ1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
See Variant Classification Assertion Criteria. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at