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NM_017882.3(CLN6):c.199-5C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Oct 4, 2021)
Last evaluated:
Jul 28, 2021
Accession:
VCV000697351.12
Variation ID:
697351
Description:
single nucleotide variant
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NM_017882.3(CLN6):c.199-5C>T

Allele ID
685408
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q23
Genomic location
15: 68214393 (GRCh38) GRCh38 UCSC
15: 68506731 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_832:g.47819C>T
LRG_832t1:c.199-5C>T
NC_000015.10:g.68214393G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000015.10:68214392:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00003
Exome Aggregation Consortium (ExAC) 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00006
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
dbSNP: rs371705916
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Dec 5, 2020 RCV001084695.2
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Jul 28, 2021 RCV000864156.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CLN6 - - GRCh38
GRCh37
446 461

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV001004918.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jul 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001149503.7
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(Jul 28, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001861597.1
Submitted: (Sep 14, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001963362.1
Submitted: (Oct 04, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001975129.1
Submitted: (Sep 21, 2021)
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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs371705916...

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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 Oct 08, 2021