17-39275069-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_032875.3(FBXL20):c.728G>T(p.Cys243Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,276 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBXL20 | ENST00000264658.11 | c.728G>T | p.Cys243Phe | missense_variant | Exon 10 of 15 | 1 | NM_032875.3 | ENSP00000264658.6 | ||
FBXL20 | ENST00000394294.7 | c.632G>T | p.Cys211Phe | missense_variant | Exon 9 of 14 | 1 | ENSP00000377832.3 | |||
FBXL20 | ENST00000577399.5 | c.734G>T | p.Cys245Phe | missense_variant | Exon 10 of 15 | 5 | ENSP00000462878.1 | |||
FBXL20 | ENST00000583610.5 | c.728G>T | p.Cys243Phe | missense_variant | Exon 10 of 16 | 2 | ENSP00000462271.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151952Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000957 AC: 24AN: 250864Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135554
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461324Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726902
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151952Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74216
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.728G>T (p.C243F) alteration is located in exon 10 (coding exon 10) of the FBXL20 gene. This alteration results from a G to T substitution at nucleotide position 728, causing the cysteine (C) at amino acid position 243 to be replaced by a phenylalanine (F). 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