chr4-155942400-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001334.3(CTSO):āc.301A>Gā(p.Met101Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000363 in 1,596,854 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 (ā ).
Frequency
Consequence
NM_001334.3 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 |
---|---|---|---|---|---|---|---|
CTSO | NM_001334.3 | c.301A>G | p.Met101Val | missense_variant | 3/8 | ENST00000433477.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTSO | ENST00000433477.4 | c.301A>G | p.Met101Val | missense_variant | 3/8 | 1 | NM_001334.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000338 AC: 8AN: 236622Hom.: 0 AF XY: 0.0000233 AC XY: 3AN XY: 128680
GnomAD4 exome AF: 0.0000339 AC: 49AN: 1444846Hom.: 0 Cov.: 29 AF XY: 0.0000334 AC XY: 24AN XY: 718894
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152008Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.301A>G (p.M101V) alteration is located in exon 3 (coding exon 3) of the CTSO gene. This alteration results from a A to G substitution at nucleotide position 301, causing the methionine (M) at amino acid position 101 to be replaced by a valine (V). 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