NM_144997.7:c.1201C>T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_144997.7(FLCN):c.1201C>T(p.Arg401Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,613,826 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_144997.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLCN | ENST00000285071.9 | c.1201C>T | p.Arg401Cys | missense_variant | Exon 11 of 14 | 1 | NM_144997.7 | ENSP00000285071.4 | ||
ENSG00000264187 | ENST00000427497.3 | n.*35C>T | non_coding_transcript_exon_variant | Exon 7 of 12 | 1 | ENSP00000394249.3 | ||||
ENSG00000264187 | ENST00000427497.3 | n.*35C>T | 3_prime_UTR_variant | Exon 7 of 12 | 1 | ENSP00000394249.3 | ||||
MPRIP | ENST00000578209.5 | c.*18-1011G>A | intron_variant | Intron 5 of 5 | 3 | ENSP00000464276.1 |
Frequencies
GnomAD3 genomes AF: 0.000348 AC: 53AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 33AN: 249280Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135100
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461550Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727088
GnomAD4 genome AF: 0.000348 AC: 53AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74466
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in a patient with spontaneous pneumothorax but does not meet diagnostic criteria for Birt-Hogg-Dub syndrome (PMID: 36410626); This variant is associated with the following publications: (PMID: 30190612, 36410626, 17028174) -
Hereditary cancer-predisposing syndrome Uncertain:1Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
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Birt-Hogg-Dube syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at