rs4660531

Variant summary

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

The NM_001291281.3(FOXO6):​c.415-7466G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,132 control chromosomes in the GnomAD database, including 5,919 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 0.26 ( 5919 hom., cov: 32)

Consequence

FOXO6
NM_001291281.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0960
Variant links:
Genes affected
FOXO6 (HGNC:24814): (forkhead box O6) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in positive regulation of dendritic spine development and regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FOXO6NM_001291281.3 linkuse as main transcriptc.415-7466G>T intron_variant ENST00000643531.4 NP_001278210.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FOXO6ENST00000641094.2 linkuse as main transcriptc.415-7466G>T intron_variant ENSP00000493184 P1
FOXO6ENST00000686812.1 linkuse as main transcriptc.30+7375G>T intron_variant ENSP00000509631
FOXO6ENST00000372591.1 linkuse as main transcriptn.424-7466G>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.265
AC:
40215
AN:
152014
Hom.:
5917
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.137
Gnomad AMI
AF:
0.439
Gnomad AMR
AF:
0.245
Gnomad ASJ
AF:
0.365
Gnomad EAS
AF:
0.172
Gnomad SAS
AF:
0.287
Gnomad FIN
AF:
0.271
Gnomad MID
AF:
0.383
Gnomad NFE
AF:
0.342
Gnomad OTH
AF:
0.273
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.264
AC:
40238
AN:
152132
Hom.:
5919
Cov.:
32
AF XY:
0.258
AC XY:
19220
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.138
Gnomad4 AMR
AF:
0.246
Gnomad4 ASJ
AF:
0.365
Gnomad4 EAS
AF:
0.172
Gnomad4 SAS
AF:
0.287
Gnomad4 FIN
AF:
0.271
Gnomad4 NFE
AF:
0.342
Gnomad4 OTH
AF:
0.273
Alfa
AF:
0.332
Hom.:
14829
Bravo
AF:
0.256
Asia WGS
AF:
0.227
AC:
785
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
4.5
DANN
Benign
0.73

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.

Other links and lift over

dbSNP: rs4660531; hg19: chr1-41839822; API