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NM_006267.5(RANBP2):c.783-6T>C

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 23, 2021)
Last evaluated:
Oct 19, 2020
Accession:
VCV000383037.8
Variation ID:
383037
Description:
single nucleotide variant
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NM_006267.5(RANBP2):c.783-6T>C

Allele ID
365310
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q13
Genomic location
2: 108740483 (GRCh38) GRCh38 UCSC
2: 109356939 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.109356939T>C
NC_000002.12:g.108740483T>C
NG_012210.1:g.26003T>C
NM_006267.5:c.783-6T>C MANE Select
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:108740482:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (C)

Allele frequency
1000 Genomes Project 0.00060
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00109
The Genome Aggregation Database (gnomAD), exomes 0.00112
The Genome Aggregation Database (gnomAD) 0.00108
Exome Aggregation Consortium (ExAC) 0.00118
Trans-Omics for Precision Medicine (TOPMed) 0.00094
Links
ClinGen: CA1822138
dbSNP: rs138540027
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 3 criteria provided, single submitter Jun 21, 2017 RCV000420242.6
Benign 1 criteria provided, single submitter Oct 19, 2020 RCV001087843.2
Benign 1 no assertion criteria provided - RCV001702774.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
RANBP2 - - GRCh38
GRCh37
639 683

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 21, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000523270.3
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.783-6 T>C variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The … (more)
Benign
(Oct 19, 2020)
criteria provided, single submitter
Method: clinical testing
Encephalopathy, acute, infection-induced, 3, suceptibility to
Allele origin: germline
Invitae
Accession: SCV000646848.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001798957.1
Submitted: (Aug 19, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001931684.1
Submitted: (Sep 23, 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: SCV001967482.1
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 rs138540027...

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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 07, 2021