chr14-77330298-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_145870.3(GSTZ1):c.475-12G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 1,606,326 control chromosomes in the GnomAD database, including 275,162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.65 ( 33817 hom., cov: 32)
Exomes 𝑓: 0.57 ( 241345 hom. )
Consequence
GSTZ1
NM_145870.3 splice_polypyrimidine_tract, intron
NM_145870.3 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00003185
2
Clinical Significance
Conservation
PhyloP100: -1.42
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 14-77330298-G-A is Benign according to our data. Variant chr14-77330298-G-A is described in ClinVar as [Benign]. Clinvar id is 1276008.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTZ1 | NM_145870.3 | c.475-12G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000216465.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTZ1 | ENST00000216465.10 | c.475-12G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_145870.3 |
Frequencies
GnomAD3 genomes ? AF: 0.651 AC: 98867AN: 151946Hom.: 33763 Cov.: 32
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GnomAD3 exomes AF: 0.572 AC: 143713AN: 251466Hom.: 42155 AF XY: 0.565 AC XY: 76850AN XY: 135906
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GnomAD4 exome AF: 0.573 AC: 832826AN: 1454262Hom.: 241345 Cov.: 32 AF XY: 0.570 AC XY: 412845AN XY: 723954
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GnomAD4 genome ? AF: 0.651 AC: 98983AN: 152064Hom.: 33817 Cov.: 32 AF XY: 0.644 AC XY: 47884AN XY: 74326
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 13, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at