17-28523792-TTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS1
The NM_001369369.1(FOXN1):c.-14-141_-14-124dupTCTCTCTCTCTCTCTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000753 in 650,488 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000043 ( 0 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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000187 (27/144350) while in subpopulation AFR AF= 0.000609 (23/37740). AF 95% confidence interval is 0.000416. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FOXN1 | NM_001369369.1 | c.-14-141_-14-124dupTCTCTCTCTCTCTCTCTC | 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_-14-163insTCTCTCTCTCTCTCTCTC | intron_variant | Intron 1 of 8 | 1 | NM_001369369.1 | ENSP00000464645.1 | |||
| RSKR | ENST00000481916.6 | n.*1196-67684_*1196-67683insGAGAGAGAGAGAGAGAGA | intron_variant | Intron 7 of 7 | 1 | ENSP00000436369.2 | ||||
| FOXN1 | ENST00000577936.2 | c.-9-169_-9-168insTCTCTCTCTCTCTCTCTC | intron_variant | Intron 1 of 8 | 4 | ENSP00000462159.2 |
Frequencies
GnomAD3 genomes 0.000187 AC: 27AN: 144250Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000435 AC: 22AN: 506138Hom.: 0 AF XY: 0.0000404 AC XY: 11AN XY: 272128
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GnomAD4 genome 0.000187 AC: 27AN: 144350Hom.: 0 Cov.: 0 AF XY: 0.000114 AC XY: 8AN XY: 69948
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at