16-695458-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_153350.4(FBXL16):c.1099G>T(p.Val367Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000166 in 1,564,680 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_153350.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBXL16 | ENST00000397621.6 | c.1099G>T | p.Val367Leu | missense_variant | Exon 3 of 6 | 5 | NM_153350.4 | ENSP00000380746.1 | ||
FBXL16 | ENST00000562648.2 | n.75G>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 1 | |||||
FBXL16 | ENST00000562563.1 | c.463G>T | p.Val155Leu | missense_variant | Exon 1 of 4 | 2 | ENSP00000455217.1 | |||
FBXL16 | ENST00000562585.1 | n.-195G>T | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152108Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000288 AC: 5AN: 173700Hom.: 0 AF XY: 0.0000209 AC XY: 2AN XY: 95498
GnomAD4 exome AF: 0.0000163 AC: 23AN: 1412572Hom.: 0 Cov.: 32 AF XY: 0.0000129 AC XY: 9AN XY: 700004
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152108Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1099G>T (p.V367L) alteration is located in exon 3 (coding exon 2) of the FBXL16 gene. This alteration results from a G to T substitution at nucleotide position 1099, causing the valine (V) at amino acid position 367 to be replaced by a leucine (L). 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