14-74734127-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_015962.5(FCF1):c.505C>T(p.Arg169Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,488 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015962.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FCF1 | NM_015962.5 | c.505C>T | p.Arg169Cys | missense_variant | Exon 7 of 8 | ENST00000341162.8 | NP_057046.1 | |
FCF1 | NM_001318508.2 | c.469C>T | p.Arg157Cys | missense_variant | Exon 7 of 8 | NP_001305437.1 | ||
FCF1 | XM_011536815.4 | c.433C>T | p.Arg145Cys | missense_variant | Exon 6 of 7 | XP_011535117.1 | ||
FCF1 | XM_011536816.4 | c.397C>T | p.Arg133Cys | missense_variant | Exon 6 of 7 | XP_011535118.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251278Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135806
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461436Hom.: 0 Cov.: 29 AF XY: 0.0000206 AC XY: 15AN XY: 727066
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.505C>T (p.R169C) alteration is located in exon 7 (coding exon 7) of the FCF1 gene. This alteration results from a C to T substitution at nucleotide position 505, causing the arginine (R) at amino acid position 169 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at