rs879255576
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP5
The NM_016122.3(CEP83):c.2075_2077delAAC(p.Gln692del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000048 in 1,459,562 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. Q692Q) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
CEP83
NM_016122.3 disruptive_inframe_deletion
NM_016122.3 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.10
Publications
1 publications found
Genes affected
CEP83 (HGNC:17966): (centrosomal protein 83) The protein encoded by this gene is a centriolar protein involved in primary cilium assembly. Defects in this gene have been associated with infantile nephronophthisis and intellectual disability. [provided by RefSeq, Oct 2016]
CEP83 Gene-Disease associations (from GenCC):
- nephronophthisis 18Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
- nephronophthisis 2Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_016122.3. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 12-94308841-AGTT-A is Pathogenic according to our data. Variant chr12-94308841-AGTT-A is described in ClinVar as Pathogenic. ClinVar VariationId is 139543.Status of the report is no_assertion_criteria_provided, 0 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_016122.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| CEP83 | MANE Select | c.2075_2077delAAC | p.Gln692del | disruptive_inframe_deletion | Exon 17 of 17 | NP_057206.2 | Q9Y592-1 | ||
| CEP83 | c.2075_2077delAAC | p.Gln692del | disruptive_inframe_deletion | Exon 16 of 16 | NP_001035858.1 | Q9Y592-1 | |||
| CEP83 | c.2075_2077delAAC | p.Gln692del | disruptive_inframe_deletion | Exon 16 of 17 | NP_001333386.1 | Q9Y592-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CEP83 | TSL:1 MANE Select | c.2075_2077delAAC | p.Gln692del | disruptive_inframe_deletion | Exon 17 of 17 | ENSP00000380911.4 | Q9Y592-1 | ||
| CEP83 | TSL:1 | c.2075_2077delAAC | p.Gln692del | disruptive_inframe_deletion | Exon 16 of 16 | ENSP00000344655.5 | Q9Y592-1 | ||
| CEP83 | c.2015_2017delAAC | p.Gln672del | disruptive_inframe_deletion | Exon 16 of 16 | ENSP00000584480.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459562Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 726210 show subpopulations
GnomAD4 exome
AF:
AC:
7
AN:
1459562
Hom.:
AF XY:
AC XY:
2
AN XY:
726210
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33396
American (AMR)
AF:
AC:
0
AN:
44688
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26074
East Asian (EAS)
AF:
AC:
0
AN:
39636
South Asian (SAS)
AF:
AC:
0
AN:
86176
European-Finnish (FIN)
AF:
AC:
0
AN:
53390
Middle Eastern (MID)
AF:
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
AC:
7
AN:
1110142
Other (OTH)
AF:
AC:
0
AN:
60304
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.511
Heterozygous variant carriers
0
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2
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4
0.00
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0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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10
<30
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35-40
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Pathogenic
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
1
-
-
Nephronophthisis 18 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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