17-28523792-TTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001369369.1(FOXN1):c.-14-135_-14-124dupTCTCTCTCTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 650,180 control chromosomes in the GnomAD database, including 5 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0033 ( 4 hom., cov: 0)
Exomes 𝑓: 0.00088 ( 1 hom. )
Consequence
FOXN1
NM_001369369.1 intron
NM_001369369.1 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0970
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00332 (479/144284) while in subpopulation AFR AF= 0.00843 (318/37702). AF 95% confidence interval is 0.00767. There are 4 homozygotes in gnomad4. There are 236 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 4 SD gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXN1 | NM_001369369.1 | c.-14-135_-14-124dupTCTCTCTCTCTC | intron_variant | Intron 1 of 8 | ENST00000579795.6 | NP_001356298.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXN1 | ENST00000579795.6 | c.-14-164_-14-163insTCTCTCTCTCTC | intron_variant | Intron 1 of 8 | 1 | NM_001369369.1 | ENSP00000464645.1 | |||
RSKR | ENST00000481916.6 | n.*1196-67684_*1196-67683insGAGAGAGAGAGA | intron_variant | Intron 7 of 7 | 1 | ENSP00000436369.2 | ||||
FOXN1 | ENST00000577936.2 | c.-9-169_-9-168insTCTCTCTCTCTC | intron_variant | Intron 1 of 8 | 4 | ENSP00000462159.2 |
Frequencies
GnomAD3 genomes AF: 0.00332 AC: 478AN: 144186Hom.: 4 Cov.: 0
GnomAD3 genomes
AF:
AC:
478
AN:
144186
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000882 AC: 446AN: 505896Hom.: 1 AF XY: 0.000908 AC XY: 247AN XY: 272026
GnomAD4 exome
AF:
AC:
446
AN:
505896
Hom.:
AF XY:
AC XY:
247
AN XY:
272026
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00332 AC: 479AN: 144284Hom.: 4 Cov.: 0 AF XY: 0.00338 AC XY: 236AN XY: 69918
GnomAD4 genome
AF:
AC:
479
AN:
144284
Hom.:
Cov.:
0
AF XY:
AC XY:
236
AN XY:
69918
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at