rs8006194

Variant summary

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

The ENST00000345097.8(FOXN3):​c.-14-32019G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,594 control chromosomes in the GnomAD database, including 18,777 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 0.49 ( 18777 hom., cov: 31)

Consequence

FOXN3
ENST00000345097.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.512
Variant links:
Genes affected
FOXN3 (HGNC:1928): (forkhead box N3) This gene is a member of the forkhead/winged helix transcription factor family. Checkpoints are eukaryotic DNA damage-inducible cell cycle arrests at G1 and G2. Checkpoint suppressor 1 suppresses multiple yeast checkpoint mutations including mec1, rad9, rad53 and dun1 by activating a MEC1-independent checkpoint pathway. Alternative splicing is observed at the locus, resulting in distinct isoforms. [provided by RefSeq, Jul 2008]

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=-0.56).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FOXN3NM_001085471.2 linkuse as main transcriptc.-14-32019G>T intron_variant NP_001078940.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FOXN3ENST00000345097.8 linkuse as main transcriptc.-14-32019G>T intron_variant 1 ENSP00000343288 P4O00409-1
FOXN3ENST00000555353.5 linkuse as main transcriptc.-14-32019G>T intron_variant 1 ENSP00000452227 A1O00409-2
FOXN3ENST00000553904.1 linkuse as main transcriptc.-14-32019G>T intron_variant 3 ENSP00000451902

Frequencies

GnomAD3 genomes
AF:
0.487
AC:
73769
AN:
151486
Hom.:
18763
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.342
Gnomad AMI
AF:
0.591
Gnomad AMR
AF:
0.625
Gnomad ASJ
AF:
0.536
Gnomad EAS
AF:
0.392
Gnomad SAS
AF:
0.601
Gnomad FIN
AF:
0.517
Gnomad MID
AF:
0.635
Gnomad NFE
AF:
0.532
Gnomad OTH
AF:
0.539
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.487
AC:
73806
AN:
151594
Hom.:
18777
Cov.:
31
AF XY:
0.491
AC XY:
36372
AN XY:
74054
show subpopulations
Gnomad4 AFR
AF:
0.342
Gnomad4 AMR
AF:
0.625
Gnomad4 ASJ
AF:
0.536
Gnomad4 EAS
AF:
0.392
Gnomad4 SAS
AF:
0.604
Gnomad4 FIN
AF:
0.517
Gnomad4 NFE
AF:
0.532
Gnomad4 OTH
AF:
0.535
Alfa
AF:
0.505
Hom.:
3573
Bravo
AF:
0.491
Asia WGS
AF:
0.456
AC:
1591
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
CADD
Benign
13
DANN
Benign
0.90

Splicing

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: rs8006194; hg19: chr14-89910853; API