rs10499051

chr6-108580977-A-G

Variant summary

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

The NM_001455.4(FOXO3):c.621+19148A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,188 control chromosomes in the GnomAD database, including 1,477 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 0.13 (1477 hom., cov: 32)
• Consequence: FOXO3 NM_001455.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXO3	NM_001455.4	c.621+19148A>G		intron_variant		ENST00000406360.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXO3	ENST00000406360.2	c.621+19148A>G		intron_variant		1	NM_001455.4	P1
FOXO3	ENST00000343882.10	c.621+19148A>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19625 AN: 152070 Hom.: 1474 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0707

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.129 AC: 19645 AN: 152188 Hom.: 1477 Cov.: 32 AF XY: 0.132 AC XY: 9854 AN XY: 74396

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0906

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0708

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.119

Alfa AF: 0.116 Hom.: 593

Bravo AF: 0.121

Asia WGS AF: 0.172 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.1
Dann	Benign	0.76

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: rs10499051; hg19: chr6-108902180;