rs4946933
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001455.4(FOXO3):c.622-3541A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,268 control chromosomes in the GnomAD database, including 66,098 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 0.93 ( 66098 hom., cov: 33)
Consequence
FOXO3
NM_001455.4 intron
NM_001455.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.925
Genes affected
FOXO3 (HGNC:3821): (forkhead box O3) This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. This gene likely functions as a trigger for apoptosis through expression of genes necessary for cell death. Translocation of this gene with the MLL gene is associated with secondary acute leukemia. Alternatively spliced transcript variants encoding the same protein have been observed. [provided by RefSeq, Jul 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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXO3 | NM_001455.4 | c.622-3541A>G | intron_variant | ENST00000406360.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXO3 | ENST00000406360.2 | c.622-3541A>G | intron_variant | 1 | NM_001455.4 | P1 | |||
FOXO3 | ENST00000343882.10 | c.622-3541A>G | intron_variant | 1 | P1 | ||||
FOXO3 | ENST00000540898.1 | c.-40+3376A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.931 AC: 141588AN: 152150Hom.: 66054 Cov.: 33
GnomAD3 genomes
?
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.931 AC: 141687AN: 152268Hom.: 66098 Cov.: 33 AF XY: 0.925 AC XY: 68854AN XY: 74450
GnomAD4 genome
?
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33
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68854
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74450
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2950
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at