rs7975
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_145870.3(GSTZ1):c.94G>A(p.Glu32Lys) variant causes a missense change. The variant allele was found at a frequency of 0.32 in 1,602,590 control chromosomes in the GnomAD database, including 83,900 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.32 ( 7778 hom., cov: 33)
Exomes 𝑓: 0.32 ( 76122 hom. )
Consequence
GSTZ1
NM_145870.3 missense
NM_145870.3 missense
Scores
1
6
9
Clinical Significance
Conservation
PhyloP100: 5.23
Genes affected
GSTZ1 (HGNC:4643): (glutathione S-transferase zeta 1) This gene is a member of the glutathione S-transferase (GSTs) super-family which encodes multifunctional enzymes important in the detoxification of electrophilic molecules, including carcinogens, mutagens, and several therapeutic drugs, by conjugation with glutathione. This enzyme catalyzes the conversion of maleylacetoacetate to fumarylacetoacatate, which is one of the steps in the phenylalanine/tyrosine degradation pathway. Deficiency of a similar gene in mouse causes oxidative stress. Several transcript variants of this gene encode multiple protein isoforms. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0017864704).
BP6
?
Variant 14-77326864-G-A is Benign according to our data. Variant chr14-77326864-G-A is described in ClinVar as [Benign]. Clinvar id is 1251643.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTZ1 | NM_145870.3 | c.94G>A | p.Glu32Lys | missense_variant | 3/9 | ENST00000216465.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTZ1 | ENST00000216465.10 | c.94G>A | p.Glu32Lys | missense_variant | 3/9 | 1 | NM_145870.3 |
Frequencies
GnomAD3 genomes ? AF: 0.316 AC: 48040AN: 152028Hom.: 7764 Cov.: 33
GnomAD3 genomes
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33
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GnomAD3 exomes AF: 0.307 AC: 73131AN: 238540Hom.: 11752 AF XY: 0.304 AC XY: 39187AN XY: 128836
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GnomAD4 exome AF: 0.320 AC: 464016AN: 1450444Hom.: 76122 Cov.: 31 AF XY: 0.317 AC XY: 228578AN XY: 720864
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GnomAD4 genome ? AF: 0.316 AC: 48070AN: 152146Hom.: 7778 Cov.: 33 AF XY: 0.315 AC XY: 23435AN XY: 74362
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1242
ESP6500AA
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1299
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36415
Asia WGS
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1195
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
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 | Jun 13, 2019 | This variant is associated with the following publications: (PMID: 22374552) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;D;D;D;T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P;P;P;P;P
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D;D;D
Sift4G
Benign
T;T;T;T;T
Vest4
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at