NM_144997.7(FLCN):c.872-13A>G AND not provided

Clinical significance:Benign (Last evaluated: May 4, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000588320.3

Allele description [Variation Report for NM_144997.7(FLCN):c.872-13A>G]

NM_144997.7(FLCN):c.872-13A>G

Gene:
FLCN:folliculin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p11.2
Genomic location:
Preferred name:
NM_144997.7(FLCN):c.872-13A>G
HGVS:
  • NC_000017.11:g.17219222T>C
  • NG_008001.2:g.22967A>G
  • NM_001353229.2:c.926-13A>G
  • NM_001353230.2:c.872-13A>G
  • NM_001353231.2:c.872-13A>G
  • NM_144997.7:c.872-13A>GMANE SELECT
  • LRG_325t1:c.872-13A>G
  • LRG_325:g.22967A>G
  • NC_000017.10:g.17122536T>C
  • NM_144997.5:c.872-13A>G
Links:
dbSNP: rs114970273
NCBI 1000 Genomes Browser:
rs114970273
Molecular consequence:
  • NM_001353229.2:c.926-13A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353230.2:c.872-13A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353231.2:c.872-13A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_144997.7:c.872-13A>G - 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
SCV000699935Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(May 4, 2016)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001892445GeneDxcriteria provided, single submitter
Benign
(Mar 3, 2015)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699935.1

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

Description

Variant summary: The FLCN variant, c.872-13A>G is located at a non-conserved intronic position, not widely known to affect splicing, with 4/5 in silico programs via Alamut predicting no significant effect on splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 608/121210 (1/199 including 12 homozygotes), which exceeds the estimated maximum expected allele frequency for a pathogenic FLCN variant of 1/769230. The variant of interest, to our knowledge, has not been reported in affected individuals via publications. A reputable clinical laboratory cites the variant as a "VOUS," although this evaluation was done prior to the availability of the ExAC population. Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.

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

From GeneDx, SCV001892445.1

#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: Nov 10, 2021

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