chr6-52836289-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000370989.7(GSTA5):c.219C>A(p.Asn73Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSTA5 | NM_153699.3 | c.219C>A | p.Asn73Lys | missense_variant | 3/6 | ENST00000370989.7 | |
GSTA5 | XM_054328422.1 | c.219C>A | p.Asn73Lys | missense_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTA5 | ENST00000370989.7 | c.219C>A | p.Asn73Lys | missense_variant | 3/6 | 1 | NM_153699.3 | P1 | |
GSTA5 | ENST00000475052.2 | c.139+1269C>A | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251470Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135912
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461626Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727154
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2024 | The c.219C>A (p.N73K) alteration is located in exon 4 (coding exon 3) of the GSTA5 gene. This alteration results from a C to A substitution at nucleotide position 219, causing the asparagine (N) at amino acid position 73 to be replaced by a lysine (K). 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