chr4-155928405-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001334.3(CTSO):c.862C>T(p.Arg288Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000416 in 1,612,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R288Q) 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 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTSO | NM_001334.3 | c.862C>T | p.Arg288Trp | missense_variant | 7/8 | ENST00000433477.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTSO | ENST00000433477.4 | c.862C>T | p.Arg288Trp | missense_variant | 7/8 | 1 | NM_001334.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250606Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135500
GnomAD4 exome AF: 0.0000418 AC: 61AN: 1460022Hom.: 0 Cov.: 30 AF XY: 0.0000344 AC XY: 25AN XY: 726328
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152012Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74244
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | The c.862C>T (p.R288W) alteration is located in exon 7 (coding exon 7) of the CTSO gene. This alteration results from a C to T substitution at nucleotide position 862, causing the arginine (R) at amino acid position 288 to be replaced by a tryptophan (W). 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