17-39299080-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_032875.3(FBXL20):c.239G>A(p.Arg80Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000808 in 1,609,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032875.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBXL20 | ENST00000264658.11 | c.239G>A | p.Arg80Gln | missense_variant | Exon 5 of 15 | 1 | NM_032875.3 | ENSP00000264658.6 | ||
FBXL20 | ENST00000394294.7 | c.239G>A | p.Arg80Gln | missense_variant | Exon 5 of 14 | 1 | ENSP00000377832.3 | |||
FBXL20 | ENST00000577399.5 | c.245G>A | p.Arg82Gln | missense_variant | Exon 5 of 15 | 5 | ENSP00000462878.1 | |||
FBXL20 | ENST00000583610.5 | c.239G>A | p.Arg80Gln | missense_variant | Exon 5 of 16 | 2 | ENSP00000462271.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248500Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134476
GnomAD4 exome AF: 0.0000837 AC: 122AN: 1457546Hom.: 0 Cov.: 30 AF XY: 0.0000690 AC XY: 50AN XY: 725122
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.239G>A (p.R80Q) alteration is located in exon 5 (coding exon 5) of the FBXL20 gene. This alteration results from a G to A substitution at nucleotide position 239, causing the arginine (R) at amino acid position 80 to be replaced by a glutamine (Q). 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