dbSNP rs1736209: ENSG00000264187:n.-487G>C (chr17-17237171-C-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000427497.3(ENSG00000264187):n.-487G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 152,062 control chromosomes in the GnomAD database, including 40,736 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.73 ( 40717 hom., cov: 31)

Exomes 𝑓: 0.80 ( 19 hom. )

Consequence

ENSG00000264187
ENST00000427497.3 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.118

Variant links:

Genes affected

ENSG00000264187 (HGNC:):

ENSG00000264187 links:

FLCN (HGNC:27310): (folliculin) This gene is located within the Smith-Magenis syndrome region on chromosome 17. Mutations in this gene are associated with Birt-Hogg-Dube syndrome, which is characterized by fibrofolliculomas, renal tumors, lung cysts, and pneumothorax. Alternative splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

FLCN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 17-17237171-C-G is Benign according to our data. Variant chr17-17237171-C-G is described in ClinVar as [Benign]. Clinvar id is 322087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-17237171-C-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLCN	NM_144997.7 link	c.-487G>C		upstream_gene_variant		ENST00000285071.9	NP_659434.2	Q8NFG4-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ENSG00000264187	ENST00000427497.3 link	n.-487G>C	non_coding_transcript_exon_variant	Exon 1 of 12	1		ENSP00000394249.3	J3QW42
ENSG00000264187	ENST00000427497.3 link	n.-487G>C	5_prime_UTR_variant	Exon 1 of 12	1		ENSP00000394249.3	J3QW42
FLCN	ENST00000285071.9 link	c.-487G>C	upstream_gene_variant		1	NM_144997.7	ENSP00000285071.4	Q8NFG4-1

Frequencies

GnomAD3 genomes

AF:

0.728

AC:

110524

AN:

151888

Hom.:

40709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.628

Gnomad AMI

AF:

0.849

Gnomad AMR

AF:

0.738

Gnomad ASJ

AF:

0.735

Gnomad EAS

AF:

0.846

Gnomad SAS

AF:

0.725

Gnomad FIN

AF:

0.874

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.753

Gnomad OTH

AF:

0.714

GnomAD4 exome

AF:

0.804

AC:

AN:

Hom.:

Cov.:

AF XY:

0.781

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.750

Gnomad4 NFE exome

AF:

0.810

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.727

AC:

110573

AN:

152006

Hom.:

40717

Cov.:

AF XY:

0.733

AC XY:

54434

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.628

Gnomad4 AMR

AF:

0.737

Gnomad4 ASJ

AF:

0.735

Gnomad4 EAS

AF:

0.846

Gnomad4 SAS

AF:

0.727

Gnomad4 FIN

AF:

0.874

Gnomad4 NFE

AF:

0.753

Gnomad4 OTH

AF:

0.711

Alfa

AF:

0.746

Hom.:

5256

Bravo

AF:

0.717

Asia WGS

AF:

0.779

AC:

2706

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 22, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

FLCN-related disorder

Benign:1

Mar 13, 2024

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Familial spontaneous pneumothorax

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: 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. -

Birt-Hogg-Dube syndrome

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.0

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over