6-52794234-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_145740.5(GSTA1):c.305T>C(p.Leu102Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000137 in 1,461,438 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L102F) has been classified as Uncertain significance.
Frequency
Consequence
NM_145740.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTA1 | NM_145740.5 | c.305T>C | p.Leu102Ser | missense_variant | 5/7 | ENST00000334575.6 | |
GSTA1 | NM_001319059.2 | c.26T>C | p.Leu9Ser | missense_variant | 4/6 | ||
GSTA1 | XM_005249034.5 | c.305T>C | p.Leu102Ser | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTA1 | ENST00000334575.6 | c.305T>C | p.Leu102Ser | missense_variant | 5/7 | 1 | NM_145740.5 | P1 | |
GSTA1 | ENST00000476213.1 | n.359T>C | non_coding_transcript_exon_variant | 4/4 | 5 | ||||
GSTA1 | ENST00000493331.5 | n.202T>C | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251348Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135832
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461438Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727066
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.305T>C (p.L102S) alteration is located in exon 5 (coding exon 4) of the GSTA1 gene. This alteration results from a T to C substitution at nucleotide position 305, causing the leucine (L) at amino acid position 102 to be replaced by a serine (S). 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