chr13-40612364-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002015.4(FOXO1):c.631-51504C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,164 control chromosomes in the GnomAD database, including 2,546 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 0.17 ( 2546 hom., cov: 32)
Consequence
FOXO1
NM_002015.4 intron
NM_002015.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.150
Genes affected
FOXO1 (HGNC:3819): (forkhead box O1) This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in myogenic growth and differentiation. Translocation of this gene with PAX3 has been associated with alveolar rhabdomyosarcoma. [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=-0.87).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXO1 | NM_002015.4 | c.631-51504C>T | intron_variant | ENST00000379561.6 | NP_002006.2 | |||
FOXO1 | XM_011535008.3 | c.87+1786C>T | intron_variant | XP_011533310.1 | ||||
FOXO1 | XM_047430204.1 | c.-82+32975C>T | intron_variant | XP_047286160.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXO1 | ENST00000379561.6 | c.631-51504C>T | intron_variant | 1 | NM_002015.4 | ENSP00000368880 | P1 | |||
FOXO1 | ENST00000655267.1 | n.334-49602C>T | intron_variant, non_coding_transcript_variant | |||||||
FOXO1 | ENST00000660760.1 | n.397+20783C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.170 AC: 25821AN: 152044Hom.: 2545 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.170 AC: 25826AN: 152164Hom.: 2546 Cov.: 32 AF XY: 0.174 AC XY: 12967AN XY: 74380
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636
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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