17-39281439-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000264658.11(FBXL20):āc.646A>Gā(p.Ile216Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,461,414 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000264658.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBXL20 | NM_032875.3 | c.646A>G | p.Ile216Val | missense_variant | 9/15 | ENST00000264658.11 | NP_116264.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBXL20 | ENST00000264658.11 | c.646A>G | p.Ile216Val | missense_variant | 9/15 | 1 | NM_032875.3 | ENSP00000264658 | P1 | |
FBXL20 | ENST00000394294.7 | c.550A>G | p.Ile184Val | missense_variant | 8/14 | 1 | ENSP00000377832 | |||
FBXL20 | ENST00000577399.5 | c.652A>G | p.Ile218Val | missense_variant | 9/15 | 5 | ENSP00000462878 | |||
FBXL20 | ENST00000583610.5 | c.646A>G | p.Ile216Val | missense_variant | 9/16 | 2 | ENSP00000462271 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250790Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135538
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461414Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 727018
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 01, 2023 | The c.646A>G (p.I216V) alteration is located in exon 9 (coding exon 9) of the FBXL20 gene. This alteration results from a A to G substitution at nucleotide position 646, causing the isoleucine (I) at amino acid position 216 to be replaced by a valine (V). 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