17-17212475-TAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAA
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_144997.7(FLCN):c.*1179delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0098 ( 7 hom., cov: 19)
Exomes 𝑓: 0.0056 ( 0 hom. )
Consequence
FLCN
NM_144997.7 3_prime_UTR
NM_144997.7 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.602
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]
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00979 (734/74958) while in subpopulation AMR AF= 0.0348 (220/6320). AF 95% confidence interval is 0.031. There are 7 homozygotes in gnomad4. There are 325 alleles in male gnomad4 subpopulation. Median coverage is 19. This position pass quality control queck.
BS2
High AC in GnomAd4 at 734 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLCN | ENST00000285071 | c.*1179delT | 3_prime_UTR_variant | Exon 14 of 14 | 1 | NM_144997.7 | ENSP00000285071.4 | |||
ENSG00000264187 | ENST00000427497.3 | n.*372+2509delT | intron_variant | Intron 9 of 11 | 1 | ENSP00000394249.3 | ||||
MPRIP | ENST00000578209.5 | c.*18-4989delA | intron_variant | Intron 5 of 5 | 3 | ENSP00000464276.1 |
Frequencies
GnomAD3 genomes AF: 0.00980 AC: 734AN: 74932Hom.: 7 Cov.: 19
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GnomAD4 exome AF: 0.00562 AC: 6AN: 1068Hom.: 0 Cov.: 0 AF XY: 0.00560 AC XY: 3AN XY: 536
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GnomAD4 genome AF: 0.00979 AC: 734AN: 74958Hom.: 7 Cov.: 19 AF XY: 0.00946 AC XY: 325AN XY: 34340
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ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at