5-108364821-T-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001163315.3(FBXL17):c.1291A>T(p.Ile431Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,612,960 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★).
Frequency
Consequence
NM_001163315.3 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 |
---|---|---|---|---|---|---|---|---|
FBXL17 | NM_001163315.3 | c.1291A>T | p.Ile431Phe | missense_variant | 3/9 | ENST00000542267.7 | NP_001156787.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBXL17 | ENST00000542267.7 | c.1291A>T | p.Ile431Phe | missense_variant | 3/9 | 1 | NM_001163315.3 | ENSP00000437464.2 | ||
FBXL17 | ENST00000496714.2 | c.298A>T | p.Ile100Phe | missense_variant | 2/7 | 1 | ENSP00000418111.2 | |||
FBXL17 | ENST00000518486.1 | n.*2A>T | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151992Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250838Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135542
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1460850Hom.: 1 Cov.: 31 AF XY: 0.0000372 AC XY: 27AN XY: 726712
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.1291A>T (p.I431F) alteration is located in exon 3 (coding exon 3) of the FBXL17 gene. This alteration results from a A to T substitution at nucleotide position 1291, causing the isoleucine (I) at amino acid position 431 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