13-40557795-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002015.4(FOXO1):c.*1254G>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 0.0422 in 152,276 control chromosomes in the GnomAD database, including 521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002015.4 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXO1 | NM_002015.4 | c.*1254G>A | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000379561.6 | NP_002006.2 | ||
FOXO1 | XM_011535008.3 | c.*1254G>A | 3_prime_UTR_variant | Exon 3 of 3 | XP_011533310.1 | |||
FOXO1 | XM_011535010.3 | c.*1254G>A | 3_prime_UTR_variant | Exon 3 of 3 | XP_011533312.1 | |||
FOXO1 | XM_047430204.1 | c.*1254G>A | 3_prime_UTR_variant | Exon 3 of 3 | XP_047286160.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0420 AC: 6385AN: 152158Hom.: 508 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 genome AF: 0.0422 AC: 6420AN: 152276Hom.: 521 Cov.: 33 AF XY: 0.0485 AC XY: 3607AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:2
- -
This variant is associated with the following publications: (PMID: 25739100) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at