20-45891598-CCTGCTGCTGCTG-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000308.4(CTSA):c.45_56delGCTGCTGCTGCT(p.Leu16_Leu19del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000278 in 1,581,938 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000308.4 disruptive_inframe_deletion
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTSA | NM_000308.4 | c.45_56delGCTGCTGCTGCT | p.Leu16_Leu19del | disruptive_inframe_deletion | Exon 2 of 15 | ENST00000646241.3 | NP_000299.3 | |
CTSA | NM_001127695.3 | c.45_56delGCTGCTGCTGCT | p.Leu16_Leu19del | disruptive_inframe_deletion | Exon 2 of 15 | NP_001121167.1 | ||
CTSA | NM_001167594.3 | c.45_56delGCTGCTGCTGCT | p.Leu16_Leu19del | disruptive_inframe_deletion | Exon 2 of 14 | NP_001161066.2 | ||
CTSA | NR_133656.2 | n.90_101delGCTGCTGCTGCT | non_coding_transcript_exon_variant | Exon 2 of 15 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000868 AC: 13AN: 149794Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.0000442 AC: 9AN: 203638Hom.: 0 AF XY: 0.0000443 AC XY: 5AN XY: 112766
GnomAD4 exome AF: 0.0000216 AC: 31AN: 1432030Hom.: 0 AF XY: 0.0000224 AC XY: 16AN XY: 712838
GnomAD4 genome AF: 0.0000867 AC: 13AN: 149908Hom.: 0 Cov.: 0 AF XY: 0.0000958 AC XY: 7AN XY: 73070
ClinVar
Submissions by phenotype
Combined deficiency of sialidase AND beta galactosidase Uncertain:1
This variant, c.99_110del, results in the deletion of 4 amino acid(s) of the CTSA protein (p.Leu34_Leu37del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CTSA-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at