14-77327990-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PS1_ModeratePP5_ModerateBP4
The NM_145870.3(GSTZ1):c.295G>A(p.Val99Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00073 in 1,614,066 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_145870.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTZ1 | NM_145870.3 | c.295G>A | p.Val99Met | missense_variant | 5/9 | ENST00000216465.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTZ1 | ENST00000216465.10 | c.295G>A | p.Val99Met | missense_variant | 5/9 | 1 | NM_145870.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000480 AC: 73AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000502 AC: 126AN: 251144Hom.: 1 AF XY: 0.000508 AC XY: 69AN XY: 135762
GnomAD4 exome AF: 0.000756 AC: 1105AN: 1461750Hom.: 4 Cov.: 33 AF XY: 0.000708 AC XY: 515AN XY: 727182
GnomAD4 genome ? AF: 0.000479 AC: 73AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000456 AC XY: 34AN XY: 74484
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | GSTZ1: PM2, PP4:Moderate, PM3:Supporting, PS3:Supporting - |
Maleylacetoacetate isomerase deficiency Other:1
Affects, no assertion criteria provided | literature only | OMIM | Jul 26, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at