chr5-41929793-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_012176.3(FBXO4):c.522G>A(p.Gln174=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,614,144 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 8 hom. )
Consequence
FBXO4
NM_012176.3 synonymous
NM_012176.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0840
Genes affected
FBXO4 (HGNC:13583): (F-box protein 4) 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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 5-41929793-G-A is Benign according to our data. Variant chr5-41929793-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2655450.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.084 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBXO4 | NM_012176.3 | c.522G>A | p.Gln174= | synonymous_variant | 3/7 | ENST00000281623.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBXO4 | ENST00000281623.8 | c.522G>A | p.Gln174= | synonymous_variant | 3/7 | 1 | NM_012176.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00118 AC: 179AN: 152178Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00166 AC: 418AN: 251434Hom.: 4 AF XY: 0.00163 AC XY: 221AN XY: 135898
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GnomAD4 exome AF: 0.00113 AC: 1656AN: 1461848Hom.: 8 Cov.: 31 AF XY: 0.00117 AC XY: 850AN XY: 727222
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GnomAD4 genome AF: 0.00118 AC: 179AN: 152296Hom.: 1 Cov.: 33 AF XY: 0.00114 AC XY: 85AN XY: 74462
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | FBXO4: BP4, BP7 - |
Computational scores
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at