11-88291569-T-TGAAAGAAAGAAAGAAAGAAA
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The ENST00000678554.1(CTSC):c.890-1063_890-1062insTTTCTTTCTTTCTTTCTTTC variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.14 ( 1825 hom., cov: 0)
Failed GnomAD Quality Control
Consequence
CTSC
ENST00000678554.1 intron, NMD_transcript
ENST00000678554.1 intron, NMD_transcript
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.799
Genes affected
CTSC (HGNC:2528): (cathepsin C) This gene encodes a member of the peptidase C1 family and lysosomal cysteine proteinase that appears to be a central coordinator for activation of many serine proteinases in cells of the immune system. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate heavy and light chains that form a disulfide-linked dimer. A portion of the propeptide acts as an intramolecular chaperone for the folding and stabilization of the mature enzyme. This enzyme requires chloride ions for activity and can degrade glucagon. Defects in the encoded protein have been shown to be a cause of Papillon-Lefevre syndrome, an autosomal recessive disorder characterized by palmoplantar keratosis and periodontitis. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTSC | ENST00000678554.1 | c.890-1063_890-1062insTTTCTTTCTTTCTTTCTTTC | intron_variant, NMD_transcript_variant | ENSP00000504541 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 17572AN: 126108Hom.: 1823 Cov.: 0 FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.139 AC: 17574AN: 126192Hom.: 1825 Cov.: 0 AF XY: 0.133 AC XY: 7988AN XY: 60168
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at