rs7208065

Positions:

• chr17-17216890-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_144997.7(FLCN):​c.1176+179A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 662,790 control chromosomes in the GnomAD database, including 98,391 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.51 (20840 hom., cov: 33)
  • Exomes 𝑓: 0.55 (77551 hom.)
• Consequence: FLCN NM_144997.7 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.123

Genes affected

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]

ENSG00000264187 (HGNC:):

MPRIP (HGNC:30321): (myosin phosphatase Rho interacting protein) Enables cadherin binding activity. Predicted to be involved in actin filament organization. Located in actin cytoskeleton and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 17-17216890-T-C is Benign according to our data. Variant chr17-17216890-T-C is described in ClinVar as [Benign]. Clinvar id is 1279818.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-17216890-T-C is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLCN	NM_144997.7	c.1176+179A>G		intron_variant		ENST00000285071.9	NP_659434.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLCN	ENST00000285071.9	c.1176+179A>G		intron_variant		1	NM_144997.7	ENSP00000285071.4
ENSG00000264187	ENST00000427497.3	n.*10+179A>G		intron_variant		1		ENSP00000394249.3
MPRIP	ENST00000578209.5	c.*18-600T>C		intron_variant		3		ENSP00000464276.1

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77904 AN: 151970 Hom.: 20835 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.476

GnomAD4 exome AF: 0.546 AC: 278799 AN: 510702 Hom.: 77551 AF XY: 0.541 AC XY: 147416 AN XY: 272616

Gnomad4 AFR exome AF: 0.372

Gnomad4 AMR exome AF: 0.571

Gnomad4 ASJ exome AF: 0.487

Gnomad4 EAS exome AF: 0.650

Gnomad4 SAS exome AF: 0.473

Gnomad4 FIN exome AF: 0.700

Gnomad4 NFE exome AF: 0.544

Gnomad4 OTH exome AF: 0.526

GnomAD4 genome AF: 0.512 AC: 77932 AN: 152088 Hom.: 20840 Cov.: 33 AF XY: 0.519 AC XY: 38619 AN XY: 74354

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.471

Alfa AF: 0.530 Hom.: 3442

Bravo AF: 0.495

Asia WGS AF: 0.595 AC: 2065 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 22, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs7208065; hg19: chr17-17120204;