17-17222388-G-A
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_144997.7(FLCN):c.779+113C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0199 in 1,465,784 control chromosomes in the GnomAD database, including 382 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.016 ( 40 hom., cov: 32)
Exomes 𝑓: 0.020 ( 342 hom. )
Consequence
FLCN
NM_144997.7 intron
NM_144997.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.137
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 17-17222388-G-A is Benign according to our data. Variant chr17-17222388-G-A is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0163 (2475/152288) while in subpopulation AMR AF= 0.0286 (438/15290). AF 95% confidence interval is 0.0264. There are 40 homozygotes in gnomad4. There are 1193 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2475 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLCN | NM_144997.7 | c.779+113C>T | intron_variant | ENST00000285071.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLCN | ENST00000285071.9 | c.779+113C>T | intron_variant | 1 | NM_144997.7 | P1 | |||
FLCN | ENST00000389169.9 | c.779+113C>T | intron_variant | 1 | |||||
FLCN | ENST00000466317.1 | n.622+113C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
FLCN | ENST00000480316.1 | n.745+113C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0162 AC: 2470AN: 152170Hom.: 40 Cov.: 32
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GnomAD4 exome AF: 0.0204 AC: 26739AN: 1313496Hom.: 342 AF XY: 0.0199 AC XY: 13011AN XY: 654298
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GnomAD4 genome AF: 0.0163 AC: 2475AN: 152288Hom.: 40 Cov.: 32 AF XY: 0.0160 AC XY: 1193AN XY: 74448
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at