5-129905308-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_175856.5(CHSY3):c.479G>A(p.Gly160Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000225 in 1,504,118 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign 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. G160A) has been classified as Uncertain significance.
Frequency
Consequence
NM_175856.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHSY3 | NM_175856.5 | c.479G>A | p.Gly160Glu | missense_variant | 1/3 | ENST00000305031.5 | |
LOC112267944 | XR_002956248.2 | n.86+534C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHSY3 | ENST00000305031.5 | c.479G>A | p.Gly160Glu | missense_variant | 1/3 | 1 | NM_175856.5 | P1 | |
ENST00000503616.5 | n.72+538C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000533 AC: 81AN: 152094Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000326 AC: 35AN: 107340Hom.: 0 AF XY: 0.000273 AC XY: 16AN XY: 58596
GnomAD4 exome AF: 0.000191 AC: 258AN: 1351916Hom.: 1 Cov.: 33 AF XY: 0.000173 AC XY: 115AN XY: 663762
GnomAD4 genome AF: 0.000532 AC: 81AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.000565 AC XY: 42AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.479G>A (p.G160E) alteration is located in exon 1 (coding exon 1) of the CHSY3 gene. This alteration results from a G to A substitution at nucleotide position 479, causing the glycine (G) at amino acid position 160 to be replaced by a glutamic acid (E). 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