17-17212475-TAAAAAAAAAAAAAAA-TAAAA
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_144997.7(FLCN):c.*1169_*1179delTTTTTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0016 in 76,042 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0016 ( 0 hom., cov: 19)
Exomes 𝑓: 0.00094 ( 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: 0.904
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 = 0.00161 (121/74974) while in subpopulation AMR AF= 0.00348 (22/6324). AF 95% confidence interval is 0.00235. There are 0 homozygotes in gnomad4. There are 52 alleles in male gnomad4 subpopulation. Median coverage is 19. This position pass quality control queck.
BS2
High AC in GnomAd4 at 121 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLCN | ENST00000285071 | c.*1169_*1179delTTTTTTTTTTT | 3_prime_UTR_variant | Exon 14 of 14 | 1 | NM_144997.7 | ENSP00000285071.4 | |||
ENSG00000264187 | ENST00000427497.3 | n.*372+2499_*372+2509delTTTTTTTTTTT | intron_variant | Intron 9 of 11 | 1 | ENSP00000394249.3 | ||||
MPRIP | ENST00000578209.5 | c.*18-4999_*18-4989delAAAAAAAAAAA | intron_variant | Intron 5 of 5 | 3 | ENSP00000464276.1 |
Frequencies
GnomAD3 genomes AF: 0.00161 AC: 121AN: 74948Hom.: 0 Cov.: 19
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GnomAD4 exome AF: 0.000936 AC: 1AN: 1068Hom.: 0 AF XY: 0.00187 AC XY: 1AN XY: 536
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GnomAD4 genome AF: 0.00161 AC: 121AN: 74974Hom.: 0 Cov.: 19 AF XY: 0.00151 AC XY: 52AN XY: 34350
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at