17-28523792-TTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001369369.1(FOXN1):c.-14-125_-14-124dupTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 647,678 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 0.014 ( 35 hom., cov: 0)
Exomes 𝑓: 0.0095 ( 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]
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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 = 0.014 (2023/144218) while in subpopulation AFR AF= 0.0325 (1225/37658). AF 95% confidence interval is 0.031. There are 35 homozygotes in gnomad4. There are 983 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 35 SD gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXN1 | NM_001369369.1 | c.-14-125_-14-124dupTC | 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_-14-163insTC | intron_variant | Intron 1 of 8 | 1 | NM_001369369.1 | ENSP00000464645.1 | |||
RSKR | ENST00000481916.6 | n.*1196-67684_*1196-67683insGA | intron_variant | Intron 7 of 7 | 1 | ENSP00000436369.2 | ||||
FOXN1 | ENST00000577936.2 | c.-9-169_-9-168insTC | intron_variant | Intron 1 of 8 | 4 | ENSP00000462159.2 |
Frequencies
GnomAD3 genomes AF: 0.0139 AC: 2010AN: 144122Hom.: 34 Cov.: 0
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GnomAD4 exome AF: 0.00950 AC: 4784AN: 503460Hom.: 1 AF XY: 0.00999 AC XY: 2704AN XY: 270666
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GnomAD4 genome AF: 0.0140 AC: 2023AN: 144218Hom.: 35 Cov.: 0 AF XY: 0.0141 AC XY: 983AN XY: 69874
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at