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NM_144997.7(FLCN):c.1463C>T (p.Ala488Val)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 2, 2021)
Last evaluated:
Dec 24, 2020
Accession:
VCV000409392.10
Variation ID:
409392
Description:
single nucleotide variant
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NM_144997.7(FLCN):c.1463C>T (p.Ala488Val)

Allele ID
401553
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17p11.2
Genomic location
17: 17215060 (GRCh38) GRCh38 UCSC
17: 17118374 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.17118374G>A
NC_000017.11:g.17215060G>A
NG_008001.2:g.27129C>T
... more HGVS
Protein change
A488V, A506V
Other names
-
Canonical SPDI
NC_000017.11:17215059:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00010
The Genome Aggregation Database (gnomAD) 0.00048
Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD), exomes 0.00016
Links
ClinGen: CA8415959
dbSNP: rs200660337
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 Sep 12, 2019 RCV000571344.2
Uncertain significance 1 criteria provided, single submitter Feb 2, 2018 RCV001124732.1
Likely benign 1 criteria provided, single submitter Dec 24, 2020 RCV001591093.3
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Nov 11, 2020 RCV000475144.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FLCN Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1149 1265

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Sep 12, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000673426.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;In silico models in agreement (benign)
Benign
(Nov 11, 2020)
criteria provided, single submitter
Method: clinical testing
Multiple fibrofolliculomas
Allele origin: germline
Invitae
Accession: SCV000549457.6
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Feb 02, 2018)
criteria provided, single submitter
Method: clinical testing
Pneumothorax, primary spontaneous
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001283717.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Feb 02, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple fibrofolliculomas
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001283718.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Dec 24, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001822719.1
Submitted: (Sep 02, 2021)
Evidence details
Comment:
Has not been previously published as pathogenic or benign to our knowledge

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 rs200660337...

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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