chr6-52836339-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000370989.7(GSTA5):c.169A>G(p.Met57Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,642 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000370989.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTA5 | NM_153699.3 | c.169A>G | p.Met57Val | missense_variant | 3/6 | ENST00000370989.7 | |
GSTA5 | XM_054328422.1 | c.169A>G | p.Met57Val | missense_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTA5 | ENST00000370989.7 | c.169A>G | p.Met57Val | missense_variant | 3/6 | 1 | NM_153699.3 | P1 | |
GSTA5 | ENST00000475052.2 | c.139+1219A>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152076Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461566Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727138
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.169A>G (p.M57V) alteration is located in exon 4 (coding exon 3) of the GSTA5 gene. This alteration results from a A to G substitution at nucleotide position 169, causing the methionine (M) at amino acid position 57 to be replaced by a valine (V). 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