rs1712
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012177.5(FBXO5):c.*433G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,700 control chromosomes in the GnomAD database, including 3,496 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.21 ( 3488 hom., cov: 32)
Exomes 𝑓: 0.12 ( 8 hom. )
Consequence
FBXO5
NM_012177.5 3_prime_UTR
NM_012177.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.638
Genes affected
FBXO5 (HGNC:13584): (F-box protein 5) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of the ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbxs class. This protein is similar to xenopus early mitotic inhibitor-1 (Emi1), which is a mitotic regulator that interacts with Cdc20 and inhibits the anaphase promoting complex. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBXO5 | NM_012177.5 | c.*433G>A | 3_prime_UTR_variant | 5/5 | ENST00000229758.8 | ||
FBXO5 | NM_001142522.3 | c.*433G>A | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBXO5 | ENST00000229758.8 | c.*433G>A | 3_prime_UTR_variant | 5/5 | 1 | NM_012177.5 | P4 | ||
FBXO5 | ENST00000367241.3 | c.*433G>A | 3_prime_UTR_variant | 5/5 | 1 | A2 | |||
FBXO5 | ENST00000477822.2 | n.2399G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.206 AC: 31341AN: 151852Hom.: 3477 Cov.: 32
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GnomAD4 exome AF: 0.124 AC: 91AN: 732Hom.: 8 Cov.: 0 AF XY: 0.148 AC XY: 56AN XY: 378
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GnomAD4 genome ? AF: 0.207 AC: 31397AN: 151968Hom.: 3488 Cov.: 32 AF XY: 0.208 AC XY: 15492AN XY: 74302
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at