chr13-40560395-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002015.4(FOXO1):c.1096A>G(p.Ser366Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S366N) has been classified as Uncertain significance.
Frequency
Consequence
NM_002015.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXO1 | NM_002015.4 | c.1096A>G | p.Ser366Gly | missense_variant | 2/3 | ENST00000379561.6 | |
FOXO1 | XM_011535008.3 | c.553A>G | p.Ser185Gly | missense_variant | 2/3 | ||
FOXO1 | XM_011535010.3 | c.385A>G | p.Ser129Gly | missense_variant | 2/3 | ||
FOXO1 | XM_047430204.1 | c.385A>G | p.Ser129Gly | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXO1 | ENST00000379561.6 | c.1096A>G | p.Ser366Gly | missense_variant | 2/3 | 1 | NM_002015.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251456Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135898
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461894Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.1096A>G (p.S366G) alteration is located in exon 2 (coding exon 2) of the FOXO1 gene. This alteration results from a A to G substitution at nucleotide position 1096, causing the serine (S) at amino acid position 366 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at