19-38948646-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_024907.7(FBXO17):c.382G>A(p.Gly128Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,613,970 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_024907.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBXO17 | NM_024907.7 | c.382G>A | p.Gly128Arg | missense_variant | Exon 3 of 6 | ENST00000292852.9 | NP_079183.4 | |
FBXO17 | NM_148169.3 | c.409G>A | p.Gly137Arg | missense_variant | Exon 3 of 6 | NP_680474.1 | ||
FBXO17 | NR_104026.2 | n.556G>A | non_coding_transcript_exon_variant | Exon 3 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBXO17 | ENST00000292852.9 | c.382G>A | p.Gly128Arg | missense_variant | Exon 3 of 6 | 1 | NM_024907.7 | ENSP00000292852.3 | ||
ENSG00000269547 | ENST00000599996.1 | c.94G>A | p.Gly32Arg | missense_variant | Exon 2 of 20 | 2 | ENSP00000472465.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251196Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135770
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461820Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727216
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.409G>A (p.G137R) alteration is located in exon 3 (coding exon 3) of the FBXO17 gene. This alteration results from a G to A substitution at nucleotide position 409, causing the glycine (G) at amino acid position 137 to be replaced by an arginine (R). 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