ClinVar Miner

Submissions for variant NM_144997.7(FLCN):c.726A>T (p.Thr242=) (rs113938514)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000082641 SCV000114683 benign not specified 2013-04-30 criteria provided, single submitter clinical testing
Ambry Genetics RCV000129668 SCV000184466 benign Hereditary cancer-predisposing syndrome 2014-06-26 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000082641 SCV000269116 benign not specified 2013-02-21 criteria provided, single submitter clinical testing Thr242Thr in exon 7 of FLCN: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. It has been identified in 5.4% (239/4406) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs113938514).
PreventionGenetics,PreventionGenetics RCV000082641 SCV000316058 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000384438 SCV000401010 benign Multiple fibrofolliculomas 2018-01-12 criteria provided, single submitter clinical testing 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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Clinical Services Laboratory,Illumina RCV000290141 SCV000401011 benign Pneumothorax, primary spontaneous 2018-01-12 criteria provided, single submitter clinical testing 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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV000384438 SCV000560336 benign Multiple fibrofolliculomas 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586027 SCV000699934 benign not provided 2016-05-04 criteria provided, single submitter clinical testing Variant summary: The c.726A>T (p.Thr242Thr) variant in FLCN affects a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice-tools in Alamut predict no significant effect on splicing, although these predictions have yet to be confirmed by functional studies. This variant is found in 2446/121198 control chromosomes (42 homozygotes) at a frequency of 0.02018, which greatly exceeds maximal expected frequency of a pathogenic allele (0.0000013), strong evidence that this variant is benign. In addition, multiple reputable clinical laboratories have classified this variant as benign. Taken together, this variant was classified as benign.

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