chr6-108675760-G-T

Position:

• chr6-108675760-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001455.4(FOXO3):​c.*35-4067G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,060 control chromosomes in the GnomAD database, including 26,506 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 0.54 (26506 hom., cov: 32)
• Consequence: FOXO3 NM_001455.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXO3	NM_001455.4	c.*35-4067G>T		intron_variant		ENST00000406360.2	NP_001446.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FOXO3	ENST00000406360.2	c.*35-4067G>T		intron_variant		1	NM_001455.4	ENSP00000385824	P1
FOXO3	ENST00000343882.10	c.*35-4067G>T		intron_variant		1		ENSP00000339527	P1
FOXO3	ENST00000540898.1	c.*35-4067G>T		intron_variant		1		ENSP00000446316

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82726 AN: 151942 Hom.: 26507 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.544 AC: 82748 AN: 152060 Hom.: 26506 Cov.: 32 AF XY: 0.543 AC XY: 40383 AN XY: 74332

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.573

Alfa AF: 0.687 Hom.: 77121

Bravo AF: 0.533

Asia WGS AF: 0.561 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.42

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

Other links and lift over

dbSNP: rs3800229; hg19: chr6-108996963;