8-67064342-C-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000262210.11(CSPP1):c.-57C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000761 in 1,577,352 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000070 ( 0 hom. )
Consequence
CSPP1
ENST00000262210.11 5_prime_UTR
ENST00000262210.11 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.393
Publications
1 publications found
Genes affected
CSPP1 (HGNC:26193): (centrosome and spindle pole associated protein 1) This gene encodes a centrosome and spindle pole associated protein. The encoded protein plays a role in cell-cycle progression and spindle organization, regulates cytokinesis, interacts with Nephrocystin 8 and is required for cilia formation. Mutations in this gene result in primary cilia abnormalities and classical Joubert syndrome. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Apr 2014]
COPS5 (HGNC:2240): (COP9 signalosome subunit 5) The protein encoded by this gene is one of the eight subunits of COP9 signalosome, a highly conserved protein complex that functions as an important regulator in multiple signaling pathways. The structure and function of COP9 signalosome is similar to that of the 19S regulatory particle of 26S proteasome. COP9 signalosome has been shown to interact with SCF-type E3 ubiquitin ligases and act as a positive regulator of E3 ubiquitin ligases. This protein is reported to be involved in the degradation of cyclin-dependent kinase inhibitor CDKN1B/p27Kip1. It is also known to be an coactivator that increases the specificity of JUN/AP1 transcription factors. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000262210.11. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CSPP1 | NM_001382391.1 | MANE Select | c.-207C>G | upstream_gene | N/A | NP_001369320.1 | A0A7I2V5W3 | ||
| CSPP1 | NM_001364869.1 | c.-57C>G | upstream_gene | N/A | NP_001351798.1 | A0A7I2PHE7 | |||
| CSPP1 | NM_024790.7 | c.-57C>G | upstream_gene | N/A | NP_079066.5 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CSPP1 | ENST00000262210.11 | TSL:1 | c.-57C>G | 5_prime_UTR | Exon 1 of 30 | ENSP00000262210.6 | A0A7I2PHE7 | ||
| CSPP1 | ENST00000675306.2 | c.-207C>G | 5_prime_UTR | Exon 1 of 28 | ENSP00000502421.1 | A0A6Q8PGS3 | |||
| CSPP1 | ENST00000678017.1 | c.-730C>G | 5_prime_UTR | Exon 1 of 25 | ENSP00000504394.1 | A0A7I2V5P5 |
Frequencies
GnomAD3 genomes 0.0000132 AC: 2AN: 152012Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152012
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: 0.00000702 AC: 10AN: 1425340Hom.: 0 Cov.: 29 AF XY: 0.0000113 AC XY: 8AN XY: 707466 show subpopulations
GnomAD4 exome
AF:
AC:
10
AN:
1425340
Hom.:
Cov.:
29
AF XY:
AC XY:
8
AN XY:
707466
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33040
American (AMR)
AF:
AC:
0
AN:
40042
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25112
East Asian (EAS)
AF:
AC:
0
AN:
39026
South Asian (SAS)
AF:
AC:
2
AN:
82980
European-Finnish (FIN)
AF:
AC:
0
AN:
45544
Middle Eastern (MID)
AF:
AC:
0
AN:
4760
European-Non Finnish (NFE)
AF:
AC:
8
AN:
1095770
Other (OTH)
AF:
AC:
0
AN:
59066
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.535
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<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 0.0000132 AC: 2AN: 152012Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74250 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152012
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
74250
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41398
American (AMR)
AF:
AC:
0
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5162
South Asian (SAS)
AF:
AC:
0
AN:
4814
European-Finnish (FIN)
AF:
AC:
0
AN:
10608
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
2
AN:
67984
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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