20-58995183-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000681011(CTSZ):c.*466T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 169,292 control chromosomes in the GnomAD database, including 32,030 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 0.61 ( 28821 hom., cov: 31)
Exomes 𝑓: 0.59 ( 3209 hom. )
Consequence
CTSZ
ENST00000681011 3_prime_UTR
ENST00000681011 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.793
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]
NELFCD (HGNC:15934): (negative elongation factor complex member C/D) The NELF complex of proteins interacts with the DSIF protein complex to repress transcriptional elongation by RNA polymerase II. The protein encoded by this gene is an essential part of the NELF complex. Alternative translation initiation site usage results in the formation of two isoforms with different N-termini. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.613 AC: 93123AN: 151818Hom.: 28813 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
93123
AN:
151818
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.589 AC: 10227AN: 17356Hom.: 3209 Cov.: 0 AF XY: 0.583 AC XY: 5122AN XY: 8782 show subpopulations
GnomAD4 exome
AF:
AC:
10227
AN:
17356
Hom.:
Cov.:
0
AF XY:
AC XY:
5122
AN XY:
8782
African (AFR)
AF:
AC:
265
AN:
512
American (AMR)
AF:
AC:
779
AN:
1490
Ashkenazi Jewish (ASJ)
AF:
AC:
301
AN:
512
East Asian (EAS)
AF:
AC:
515
AN:
636
South Asian (SAS)
AF:
AC:
831
AN:
1386
European-Finnish (FIN)
AF:
AC:
301
AN:
576
Middle Eastern (MID)
AF:
AC:
23
AN:
44
European-Non Finnish (NFE)
AF:
AC:
6672
AN:
11240
Other (OTH)
AF:
AC:
540
AN:
960
Heterozygous variant carriers
0
199
397
596
794
993
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
78
156
234
312
390
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.613 AC: 93180AN: 151936Hom.: 28821 Cov.: 31 AF XY: 0.610 AC XY: 45327AN XY: 74246 show subpopulations
GnomAD4 genome
AF:
AC:
93180
AN:
151936
Hom.:
Cov.:
31
AF XY:
AC XY:
45327
AN XY:
74246
African (AFR)
AF:
AC:
23097
AN:
41412
American (AMR)
AF:
AC:
8978
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
AC:
2114
AN:
3464
East Asian (EAS)
AF:
AC:
4076
AN:
5170
South Asian (SAS)
AF:
AC:
3117
AN:
4816
European-Finnish (FIN)
AF:
AC:
6232
AN:
10506
Middle Eastern (MID)
AF:
AC:
150
AN:
294
European-Non Finnish (NFE)
AF:
AC:
43502
AN:
67990
Other (OTH)
AF:
AC:
1266
AN:
2114
Heterozygous variant carriers
0
1820
3640
5461
7281
9101
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
776
1552
2328
3104
3880
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2345
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at