GeneBe

rs11296619

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001382391.1(CSPP1):​c.2128+22_2128+36delTTTTTTTTTTTTTTT variant causes a intron change. The variant allele was found at a frequency of 0.00000667 in 1,049,696 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000067 ( 0 hom. )

Consequence

CSPP1
NM_001382391.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.17

Publications

0 publications found
Variant links:
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]
CSPP1 Gene-Disease associations (from GenCC):
  • Joubert syndrome 21
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P
  • Joubert syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • Joubert syndrome with Jeune asphyxiating thoracic dystrophy
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • Meckel syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CSPP1NM_001382391.1 linkc.2128+22_2128+36delTTTTTTTTTTTTTTT intron_variant Intron 18 of 30 ENST00000678616.1 NP_001369320.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CSPP1ENST00000678616.1 linkc.2128+22_2128+36delTTTTTTTTTTTTTTT intron_variant Intron 18 of 30 NM_001382391.1 ENSP00000504733.1 A0A7I2V5W3

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000667
AC:
7
AN:
1049696
Hom.:
0
AF XY:
0.00000965
AC XY:
5
AN XY:
517928
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
22100
American (AMR)
AF:
0.00
AC:
0
AN:
17998
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15356
East Asian (EAS)
AF:
0.00
AC:
0
AN:
29252
South Asian (SAS)
AF:
0.00
AC:
0
AN:
43176
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
36256
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3248
European-Non Finnish (NFE)
AF:
0.00000834
AC:
7
AN:
839220
Other (OTH)
AF:
0.00
AC:
0
AN:
43090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.439
Heterozygous variant carriers
0
1
1
2
2
3
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
Cov.:
0
Alfa
AF:
0.00
Hom.:
1063

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
4.2

Splicing

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

Publications

Other links and lift over

dbSNP: rs11296619; hg19: chr8-68062182; API