chr5-129905110-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.281G>A(p.Gly94Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000364 in 1,540,000 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G94R) 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.281G>A | p.Gly94Glu | missense_variant | 1/3 | ENST00000305031.5 | |
LOC112267944 | XR_002956248.2 | n.86+732C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHSY3 | ENST00000305031.5 | c.281G>A | p.Gly94Glu | missense_variant | 1/3 | 1 | NM_175856.5 | P1 | |
ENST00000503616.5 | n.72+736C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152148Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000895 AC: 12AN: 134050Hom.: 0 AF XY: 0.0000946 AC XY: 7AN XY: 73986
GnomAD4 exome AF: 0.0000389 AC: 54AN: 1387852Hom.: 0 Cov.: 31 AF XY: 0.0000496 AC XY: 34AN XY: 685698
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152148Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at