13-40559985-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002015.4(FOXO1):c.1506G>A(p.Ser502Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,614,024 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002015.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXO1 | NM_002015.4 | c.1506G>A | p.Ser502Ser | synonymous_variant | Exon 2 of 3 | ENST00000379561.6 | NP_002006.2 | |
FOXO1 | XM_011535008.3 | c.963G>A | p.Ser321Ser | synonymous_variant | Exon 2 of 3 | XP_011533310.1 | ||
FOXO1 | XM_011535010.3 | c.795G>A | p.Ser265Ser | synonymous_variant | Exon 2 of 3 | XP_011533312.1 | ||
FOXO1 | XM_047430204.1 | c.795G>A | p.Ser265Ser | synonymous_variant | Exon 2 of 3 | XP_047286160.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00130 AC: 197AN: 152058Hom.: 5 Cov.: 31
GnomAD3 exomes AF: 0.00259 AC: 650AN: 251290Hom.: 9 AF XY: 0.00272 AC XY: 369AN XY: 135812
GnomAD4 exome AF: 0.00148 AC: 2163AN: 1461848Hom.: 34 Cov.: 32 AF XY: 0.00163 AC XY: 1183AN XY: 727226
GnomAD4 genome AF: 0.00127 AC: 194AN: 152176Hom.: 5 Cov.: 31 AF XY: 0.00126 AC XY: 94AN XY: 74378
ClinVar
Submissions by phenotype
not provided Benign:2
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FOXO1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at