rs13720
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001336.4(CTSZ):c.*136C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 703,528 control chromosomes in the GnomAD database, including 234,419 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.83 ( 51985 hom., cov: 31)
Exomes 𝑓: 0.81 ( 182434 hom. )
Consequence
CTSZ
NM_001336.4 3_prime_UTR
NM_001336.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.71
Genes affected
CTSZ (HGNC:2547): (cathepsin Z) The protein encoded by this gene is a lysosomal cysteine proteinase and member of the peptidase C1 family. It exhibits both carboxy-monopeptidase and carboxy-dipeptidase activities. The encoded protein has also been known as cathepsin X and cathepsin P. This gene is expressed ubiquitously in cancer cell lines and primary tumors and, like other members of this family, may be involved in tumorigenesis. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTSZ | NM_001336.4 | c.*136C>T | 3_prime_UTR_variant | 6/6 | ENST00000217131.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTSZ | ENST00000217131.6 | c.*136C>T | 3_prime_UTR_variant | 6/6 | 1 | NM_001336.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.825 AC: 125406AN: 151966Hom.: 51924 Cov.: 31
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GnomAD4 exome AF: 0.813 AC: 448099AN: 551444Hom.: 182434 Cov.: 7 AF XY: 0.813 AC XY: 235335AN XY: 289632
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GnomAD4 genome ? AF: 0.825 AC: 125525AN: 152084Hom.: 51985 Cov.: 31 AF XY: 0.827 AC XY: 61459AN XY: 74336
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at