17-28523792-TTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TTCTCTCTCTC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001369369.1(FOXN1):​c.-14-141_-14-124delTCTCTCTCTCTCTCTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0468 in 568,938 control chromosomes in the GnomAD database, including 36 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00053 ( 1 hom., cov: 0)
Exomes 𝑓: 0.062 ( 35 hom. )

Consequence

FOXN1
NM_001369369.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.129
Variant links:
Genes affected
FOXN1 (HGNC:12765): (forkhead box N1) Mutations in the winged-helix transcription factor gene at the nude locus in mice and rats produce the pleiotropic phenotype of hairlessness and athymia, resulting in a severely compromised immune system. This gene is orthologous to the mouse and rat genes and encodes a similar DNA-binding transcription factor that is thought to regulate keratin gene expression. A mutation in this gene has been correlated with T-cell immunodeficiency, the skin disorder congenital alopecia, and nail dystrophy. Alternative splicing in the 5' UTR of this gene has been observed. [provided by RefSeq, Jul 2008]
RSKR (HGNC:26314): (ribosomal protein S6 kinase related) Predicted to enable protein kinase activity. Predicted to be involved in protein phosphorylation. [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 -8 ACMG points.

BA1
GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0689 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FOXN1NM_001369369.1 linkc.-14-141_-14-124delTCTCTCTCTCTCTCTCTC intron_variant Intron 1 of 8 ENST00000579795.6 NP_001356298.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FOXN1ENST00000579795.6 linkc.-14-163_-14-146delTCTCTCTCTCTCTCTCTC intron_variant Intron 1 of 8 1 NM_001369369.1 ENSP00000464645.1 O15353
RSKRENST00000481916.6 linkn.*1196-67701_*1196-67684delGAGAGAGAGAGAGAGAGA intron_variant Intron 7 of 7 1 ENSP00000436369.2 Q96LW2-2
FOXN1ENST00000577936.2 linkc.-9-168_-9-151delTCTCTCTCTCTCTCTCTC intron_variant Intron 1 of 8 4 ENSP00000462159.2 O15353J3KRT9

Frequencies

GnomAD3 genomes
AF:
0.000535
AC:
77
AN:
143848
Hom.:
1
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00120
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000210
Gnomad ASJ
AF:
0.000292
Gnomad EAS
AF:
0.000209
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000631
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000300
Gnomad OTH
AF:
0.000508
GnomAD4 exome
AF:
0.0624
AC:
26534
AN:
424994
Hom.:
35
AF XY:
0.0628
AC XY:
14367
AN XY:
228936
show subpopulations
Gnomad4 AFR exome
AF:
0.0201
Gnomad4 AMR exome
AF:
0.0420
Gnomad4 ASJ exome
AF:
0.0679
Gnomad4 EAS exome
AF:
0.0583
Gnomad4 SAS exome
AF:
0.0523
Gnomad4 FIN exome
AF:
0.0602
Gnomad4 NFE exome
AF:
0.0698
Gnomad4 OTH exome
AF:
0.0594
GnomAD4 genome
AF:
0.000535
AC:
77
AN:
143944
Hom.:
1
Cov.:
0
AF XY:
0.000517
AC XY:
36
AN XY:
69688
show subpopulations
Gnomad4 AFR
AF:
0.00119
Gnomad4 AMR
AF:
0.000210
Gnomad4 ASJ
AF:
0.000292
Gnomad4 EAS
AF:
0.000210
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000631
Gnomad4 NFE
AF:
0.000300
Gnomad4 OTH
AF:
0.000503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs10527420; hg19: chr17-26850810; API