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NM_025114.4(CEP290):c.3574-9del

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
14 (Most recent: Aug 23, 2021)
Last evaluated:
Jul 22, 2021
Accession:
VCV000096170.7
Variation ID:
96170
Description:
1bp deletion
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NM_025114.4(CEP290):c.3574-9del

Allele ID
102064
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
12q21.32
Genomic location
12: 88089496 (GRCh38) GRCh38 UCSC
12: 88483273 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_025114.3:c.3574-9delT
NC_000012.11:g.88483280del
NC_000012.12:g.88089503del
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000012.12:88089495:AAAAAAAA:AAAAAAA
Functional consequence
-
Global minor allele frequency (GMAF)
0.12640 (AAAAAAAA)

Allele frequency
-
Links
ClinGen: CA149313
dbSNP: rs10717563
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Nov 20, 2013 RCV000082247.5
Benign 2 criteria provided, single submitter Jun 14, 2016 RCV000268851.3
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000307583.2
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000313246.2
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000364690.2
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000370292.2
Benign 1 criteria provided, single submitter Jun 11, 2018 RCV000827178.3
Benign 1 criteria provided, single submitter Nov 25, 2020 RCV001080740.2
Benign 1 criteria provided, single submitter Jul 22, 2021 RCV001579180.1
Benign 1 criteria provided, single submitter Jul 22, 2021 RCV001579181.1
Benign 1 criteria provided, single submitter Jul 22, 2021 RCV001579182.1
Benign 1 criteria provided, single submitter Jul 22, 2021 RCV001579183.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CEP290 - - GRCh38
GRCh37
1440 1516

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jun 11, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000968806.1
Submitted: (Apr 12, 2019)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Bardet-Biedl syndrome 14
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001806608.1
Submitted: (Aug 23, 2021)
Evidence details
Benign
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Joubert syndrome 5
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001806609.1
Submitted: (Aug 23, 2021)
Evidence details
Benign
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Meckel syndrome, type 4
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001806610.1
Submitted: (Aug 23, 2021)
Evidence details
Benign
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Senior-Loken syndrome 6
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001806611.1
Submitted: (Aug 23, 2021)
Evidence details
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000314547.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Senior-Loken Syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000381501.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Bardet-Biedl Syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000381498.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Leber Congenital Amaurosis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000381499.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Joubert Syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000381500.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Meckel Syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000381497.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Nov 20, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000114196.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Joubert syndrome
Meckel-Gruber syndrome
Nephronophthisis
Allele origin: germline
Invitae
Accession: SCV000252869.8
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Leber congenital amaurosis
Allele origin: germline
Natera, Inc.
Accession: SCV001452845.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CEP290 - - - -

Text-mined citations for rs10717563...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2021