17-28523792-TTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TTCTCTCTCTCTCTC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001369369.1(FOXN1):c.-14-137_-14-124delTCTCTCTCTCTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00216 in 649,958 control chromosomes in the GnomAD database, including 11 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0019 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0022 ( 11 hom. )
Consequence
FOXN1
NM_001369369.1 intron
NM_001369369.1 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.129
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 sas. gnomad4 allele frequency = 0.00188 (272/144356) while in subpopulation SAS AF= 0.00811 (36/4440). AF 95% confidence interval is 0.00602. There are 0 homozygotes in gnomad4. There are 143 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 11 SD gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXN1 | NM_001369369.1 | c.-14-137_-14-124delTCTCTCTCTCTCTC | 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_-14-150delTCTCTCTCTCTCTC | intron_variant | Intron 1 of 8 | 1 | NM_001369369.1 | ENSP00000464645.1 | |||
RSKR | ENST00000481916.6 | n.*1196-67697_*1196-67684delGAGAGAGAGAGAGA | intron_variant | Intron 7 of 7 | 1 | ENSP00000436369.2 | ||||
FOXN1 | ENST00000577936.2 | c.-9-168_-9-155delTCTCTCTCTCTCTC | intron_variant | Intron 1 of 8 | 4 | ENSP00000462159.2 |
Frequencies
GnomAD3 genomes AF: 0.00189 AC: 272AN: 144256Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00224 AC: 1131AN: 505602Hom.: 11 AF XY: 0.00268 AC XY: 729AN XY: 271846
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GnomAD4 genome AF: 0.00188 AC: 272AN: 144356Hom.: 0 Cov.: 0 AF XY: 0.00204 AC XY: 143AN XY: 69950
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at