1-206022267-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001910.4(CTSE):c.226A>G(p.Met76Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000936 in 1,601,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001910.4 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTSE | NM_001910.4 | c.226A>G | p.Met76Val | missense_variant, splice_region_variant | 3/9 | ENST00000358184.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTSE | ENST00000358184.7 | c.226A>G | p.Met76Val | missense_variant, splice_region_variant | 3/9 | 1 | NM_001910.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151714Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248144Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134026
GnomAD4 exome AF: 0.00000828 AC: 12AN: 1450072Hom.: 0 Cov.: 27 AF XY: 0.00000693 AC XY: 5AN XY: 721656
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151714Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74020
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.226A>G (p.M76V) alteration is located in exon 3 (coding exon 3) of the CTSE gene. This alteration results from a A to G substitution at nucleotide position 226, causing the methionine (M) at amino acid position 76 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