Variant rs1334241 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002015.4(FOXO1):c.630+16610G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,116 control chromosomes in the GnomAD database, including 2,990 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 0.19 ( 2990 hom., cov: 32)

Consequence

FOXO1
NM_002015.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.510

Variant links:

Genes affected

FOXO1 (HGNC:3819): (forkhead box O1) This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in myogenic growth and differentiation. Translocation of this gene with PAX3 has been associated with alveolar rhabdomyosarcoma. [provided by RefSeq, Jul 2008]

FOXO1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FOXO1	NM_002015.4 link	c.630+16610G>A		intron_variant		ENST00000379561.6	NP_002006.2	Q12778
FOXO1	XM_047430204.1 link	c.-3716G>A		5_prime_UTR_variant	1/3		XP_047286160.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
FOXO1	ENST00000379561.6 link	c.630+16610G>A	intron_variant	1	NM_002015.4	ENSP00000368880.4	Q12778
FOXO1	ENST00000655267.1 link	n.333+16610G>A	intron_variant
FOXO1	ENST00000660760.1 link	n.296-15725G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.193

AC:

29350

AN:

151998

Hom.:

2986

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.210

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.0946

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.176

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

GnomAD4 genome

AF:

0.193

AC:

29371

AN:

152116

Hom.:

2990

Cov.:

AF XY:

0.197

AC XY:

14631

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.160

Gnomad4 AMR

AF:

0.210

Gnomad4 ASJ

AF:

0.160

Gnomad4 EAS

AF:

0.0942

Gnomad4 SAS

AF:

0.295

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.207

Gnomad4 OTH

AF:

0.173

Alfa

AF:

0.200

Hom.:

6195

Bravo

AF:

0.187

Asia WGS

AF:

0.192

AC:

667

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.9

DANN

Benign

0.63

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