chr6-52900073-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_000847.5(GSTA3):āc.275T>Cā(p.Ile92Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000138 in 1,444,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_000847.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTA3 | NM_000847.5 | c.275T>C | p.Ile92Thr | missense_variant, splice_region_variant | 5/7 | ENST00000211122.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTA3 | ENST00000211122.4 | c.275T>C | p.Ile92Thr | missense_variant, splice_region_variant | 5/7 | 1 | NM_000847.5 | P1 | |
GSTA3 | ENST00000370968.5 | c.125T>C | p.Ile42Thr | missense_variant, splice_region_variant | 4/6 | 1 | |||
GSTA3 | ENST00000431899.2 | c.125T>C | p.Ile42Thr | missense_variant, splice_region_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000427 AC: 1AN: 234078Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 126532
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1444742Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 717758
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 21, 2021 | The c.275T>C (p.I92T) alteration is located in exon 5 (coding exon 4) of the GSTA3 gene. This alteration results from a T to C substitution at nucleotide position 275, causing the isoleucine (I) at amino acid position 92 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at