Variant 6-108652895-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001455.4(FOXO3):c.622-10560C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,022 control chromosomes in the GnomAD database, including 26,563 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 0.56 ( 26563 hom., cov: 31)

Consequence

FOXO3
NM_001455.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.169

Variant links:

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]

FOXO3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXO3	NM_001455.4 link	c.622-10560C>T		intron_variant		ENST00000406360.2	NP_001446.1	O43524-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXO3	ENST00000406360.2 link	c.622-10560C>T		intron_variant		1	NM_001455.4	ENSP00000385824.1		O43524-1
FOXO3	ENST00000343882.10 link	c.622-10560C>T		intron_variant		1		ENSP00000339527.6		O43524-1

Frequencies

GnomAD3 genomes

AF:

0.559

AC:

84963

AN:

151904

Hom.:

26557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.786

Gnomad AMR

AF:

0.640

Gnomad ASJ

AF:

0.741

Gnomad EAS

AF:

0.694

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.694

Gnomad OTH

AF:

0.574

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.559

AC:

85010

AN:

152022

Hom.:

26563

Cov.:

AF XY:

0.558

AC XY:

41460

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.260

Gnomad4 AMR

AF:

0.640

Gnomad4 ASJ

AF:

0.741

Gnomad4 EAS

AF:

0.694

Gnomad4 SAS

AF:

0.530

Gnomad4 FIN

AF:

0.614

Gnomad4 NFE

AF:

0.694

Gnomad4 OTH

AF:

0.576

Alfa

AF:

0.609

Hom.:

3742

Bravo

AF:

0.550

Asia WGS

AF:

0.557

AC:

1937

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

3.7

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over