GeneBe

rs10527420

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001369369.1(FOXN1):​c.-14-151_-14-124delTCTCTCTCTCTCTCTCTCTCTCTCTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000020 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FOXN1
NM_001369369.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.129

Publications

1 publications found
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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001369369.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FOXN1
NM_001369369.1
MANE Select
c.-14-151_-14-124delTCTCTCTCTCTCTCTCTCTCTCTCTCTC
intron
N/ANP_001356298.1O15353
FOXN1
NM_003593.3
c.-177_-150delTCTCTCTCTCTCTCTCTCTCTCTCTCTC
upstream_gene
N/ANP_003584.2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FOXN1
ENST00000579795.6
TSL:1 MANE Select
c.-14-163_-14-136delTCTCTCTCTCTCTCTCTCTCTCTCTCTC
intron
N/AENSP00000464645.1O15353
RSKR
ENST00000481916.6
TSL:1
n.*1196-67711_*1196-67684delGAGAGAGAGAGAGAGAGAGAGAGAGAGA
intron
N/AENSP00000436369.2Q96LW2-2
FOXN1
ENST00000577936.2
TSL:4
c.-9-168_-9-141delTCTCTCTCTCTCTCTCTCTCTCTCTCTC
intron
N/AENSP00000462159.2O15353

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000198
AC:
1
AN:
506164
Hom.:
0
AF XY:
0.00000367
AC XY:
1
AN XY:
272142
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
14056
American (AMR)
AF:
0.0000356
AC:
1
AN:
28078
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
17594
East Asian (EAS)
AF:
0.00
AC:
0
AN:
30854
South Asian (SAS)
AF:
0.00
AC:
0
AN:
57046
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
35504
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2412
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
292622
Other (OTH)
AF:
0.00
AC:
0
AN:
27998
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs10527420; hg19: chr17-26850810; API