NM_006267.5(RANBP2):c.783-6T>C AND not provided

Clinical significance:Uncertain significance (Last evaluated: Jun 21, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000420242.6

Allele description [Variation Report for NM_006267.5(RANBP2):c.783-6T>C]

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

Gene:
RANBP2:RAN binding protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q13
Genomic location:
Preferred name:
NM_006267.5(RANBP2):c.783-6T>C
HGVS:
  • NC_000002.12:g.108740483T>C
  • NG_012210.1:g.26003T>C
  • NM_006267.5:c.783-6T>CMANE SELECT
  • NC_000002.11:g.109356939T>C
  • NM_006267.4:c.783-6T>C
Links:
dbSNP: rs138540027
NCBI 1000 Genomes Browser:
rs138540027
Molecular consequence:
  • NM_006267.5:c.783-6T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000523270GeneDxcriteria provided, single submitter
Uncertain significance
(Jun 21, 2017)
germlineclinical testing

Citation Link,

SCV001798957Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensusno assertion criteria providedLikely benigngermlineclinical testing

SCV001967482Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedLikely benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000523270.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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 c.783-6 T>C variant is observed in 106/64806 (0.16%) alleles from individuals of European background, including 1 homozygous individual in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The c.783-6 T>C substitution occurs at a position that is conserved across species. In-silico splice prediction models are inconsistent in their predictions as to whether or not c.783-6 T>C results in abnormal gene splicing, and in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001798957.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001967482.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 6, 2021

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