rs779028759
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_144997.7(FLCN):c.1539-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_144997.7 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLCN | NM_144997.7 | c.1539-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000285071.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLCN | ENST00000285071.9 | c.1539-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_144997.7 | P1 | |||
MPRIP | ENST00000578209.5 | c.*18-3628G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 251110Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135716
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461628Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727106
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74364
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Sep 13, 2022 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
Birt-Hogg-Dube syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at