17-28523792-TTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TTCTCTCTCTCTCTCTCTCTCTCTC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001369369.1(FOXN1):c.-14-127_-14-124delTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00377 in 649,812 control chromosomes in the GnomAD database, including 9 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0049 ( 6 hom., cov: 0)
Exomes 𝑓: 0.0035 ( 3 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 = 0.0049 (707/144330) while in subpopulation AFR AF= 0.00917 (346/37732). AF 95% confidence interval is 0.00837. There are 6 homozygotes in gnomad4. There are 326 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 SD gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXN1 | NM_001369369.1 | c.-14-127_-14-124delTCTC | 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.-14-163_-14-160delTCTC | intron_variant | Intron 1 of 8 | 1 | NM_001369369.1 | ENSP00000464645.1 | |||
RSKR | ENST00000481916.6 | n.*1196-67687_*1196-67684delGAGA | intron_variant | Intron 7 of 7 | 1 | ENSP00000436369.2 | ||||
FOXN1 | ENST00000577936.2 | c.-9-168_-9-165delTCTC | intron_variant | Intron 1 of 8 | 4 | ENSP00000462159.2 |
Frequencies
GnomAD3 genomes AF: 0.00490 AC: 707AN: 144230Hom.: 6 Cov.: 0
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GnomAD4 exome AF: 0.00345 AC: 1745AN: 505482Hom.: 3 AF XY: 0.00357 AC XY: 971AN XY: 271784
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GnomAD4 genome AF: 0.00490 AC: 707AN: 144330Hom.: 6 Cov.: 0 AF XY: 0.00466 AC XY: 326AN XY: 69934
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at