4-155928404-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001334.3(CTSO):c.863G>A(p.Arg288Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,612,444 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R288W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001334.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTSO | NM_001334.3 | c.863G>A | p.Arg288Gln | missense_variant | 7/8 | ENST00000433477.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTSO | ENST00000433477.4 | c.863G>A | p.Arg288Gln | missense_variant | 7/8 | 1 | NM_001334.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250742Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135550
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1460366Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 726482
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2023 | The c.863G>A (p.R288Q) alteration is located in exon 7 (coding exon 7) of the CTSO gene. This alteration results from a G to A substitution at nucleotide position 863, causing the arginine (R) at amino acid position 288 to be replaced by a glutamine (Q). 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