chr14-77327940-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_145870.3(GSTZ1):āc.245T>Cā(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 (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M82I) has been classified as Uncertain significance.
Frequency
Consequence
NM_145870.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTZ1 | NM_145870.3 | c.245T>C | p.Met82Thr | missense_variant | 5/9 | ENST00000216465.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTZ1 | ENST00000216465.10 | c.245T>C | p.Met82Thr | missense_variant | 5/9 | 1 | NM_145870.3 |
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
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 16, 2020 | 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
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 30, 2023 | See Variant Classification Assertion Criteria. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at