5-129908128-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_175856.5(CHSY3):c.854A>T(p.Tyr285Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000545 in 1,614,198 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_175856.5 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 |
---|---|---|---|---|---|---|---|
CHSY3 | NM_175856.5 | c.854A>T | p.Tyr285Phe | missense_variant | 2/3 | ENST00000305031.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHSY3 | ENST00000305031.5 | c.854A>T | p.Tyr285Phe | missense_variant | 2/3 | 1 | NM_175856.5 | P1 | |
CHSY3 | ENST00000507545.1 | n.42A>T | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000954 AC: 24AN: 251464Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135906
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727244
GnomAD4 genome AF: 0.000263 AC: 40AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 12, 2024 | The c.854A>T (p.Y285F) alteration is located in exon 2 (coding exon 2) of the CHSY3 gene. This alteration results from a A to T substitution at nucleotide position 854, causing the tyrosine (Y) at amino acid position 285 to be replaced by a phenylalanine (F). 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