chr20-58996708-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000217131.6(CTSZ):ā€‹c.732T>Cā€‹(p.Ser244=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 1,613,790 control chromosomes in the GnomAD database, including 334,683 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: š‘“ 0.66 ( 33569 hom., cov: 32)
Exomes š‘“: 0.64 ( 301114 hom. )

Consequence

CTSZ
ENST00000217131.6 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.83
Variant links:
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 -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP7
Synonymous conserved (PhyloP=-3.83 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CTSZNM_001336.4 linkuse as main transcriptc.732T>C p.Ser244= synonymous_variant 5/6 ENST00000217131.6 NP_001327.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CTSZENST00000217131.6 linkuse as main transcriptc.732T>C p.Ser244= synonymous_variant 5/61 NM_001336.4 ENSP00000217131 P1

Frequencies

GnomAD3 genomes
AF:
0.662
AC:
100565
AN:
151986
Hom.:
33539
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.724
Gnomad AMI
AF:
0.712
Gnomad AMR
AF:
0.606
Gnomad ASJ
AF:
0.609
Gnomad EAS
AF:
0.788
Gnomad SAS
AF:
0.652
Gnomad FIN
AF:
0.595
Gnomad MID
AF:
0.494
Gnomad NFE
AF:
0.641
Gnomad OTH
AF:
0.634
GnomAD3 exomes
AF:
0.635
AC:
159785
AN:
251458
Hom.:
51360
AF XY:
0.635
AC XY:
86361
AN XY:
135896
show subpopulations
Gnomad AFR exome
AF:
0.727
Gnomad AMR exome
AF:
0.562
Gnomad ASJ exome
AF:
0.614
Gnomad EAS exome
AF:
0.785
Gnomad SAS exome
AF:
0.642
Gnomad FIN exome
AF:
0.584
Gnomad NFE exome
AF:
0.631
Gnomad OTH exome
AF:
0.621
GnomAD4 exome
AF:
0.641
AC:
936527
AN:
1461686
Hom.:
301114
Cov.:
47
AF XY:
0.640
AC XY:
465458
AN XY:
727156
show subpopulations
Gnomad4 AFR exome
AF:
0.726
Gnomad4 AMR exome
AF:
0.570
Gnomad4 ASJ exome
AF:
0.611
Gnomad4 EAS exome
AF:
0.801
Gnomad4 SAS exome
AF:
0.645
Gnomad4 FIN exome
AF:
0.593
Gnomad4 NFE exome
AF:
0.638
Gnomad4 OTH exome
AF:
0.644
GnomAD4 genome
AF:
0.662
AC:
100660
AN:
152104
Hom.:
33569
Cov.:
32
AF XY:
0.658
AC XY:
48932
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.724
Gnomad4 AMR
AF:
0.606
Gnomad4 ASJ
AF:
0.609
Gnomad4 EAS
AF:
0.788
Gnomad4 SAS
AF:
0.653
Gnomad4 FIN
AF:
0.595
Gnomad4 NFE
AF:
0.641
Gnomad4 OTH
AF:
0.633
Alfa
AF:
0.635
Hom.:
49941
Bravo
AF:
0.667
Asia WGS
AF:
0.692
AC:
2409
AN:
3478
EpiCase
AF:
0.623
EpiControl
AF:
0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.13
DANN
Benign
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9760; hg19: chr20-57571763; API