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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0970
Variant links:
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]
RSKR (HGNC:26314): (ribosomal protein S6 kinase related) Predicted to enable protein kinase activity. Predicted to be involved in protein phosphorylation. [provided by Alliance of Genome Resources, Apr 2022]

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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 = 0.00332 (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
FOXN1NM_001369369.1 linkc.-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
FOXN1ENST00000579795.6 linkc.-14-164_-14-163insTCTCTCTCTCTC intron_variant Intron 1 of 8 1 NM_001369369.1 ENSP00000464645.1 O15353
RSKRENST00000481916.6 linkn.*1196-67684_*1196-67683insGAGAGAGAGAGA intron_variant Intron 7 of 7 1 ENSP00000436369.2 Q96LW2-2
FOXN1ENST00000577936.2 linkc.-9-169_-9-168insTCTCTCTCTCTC intron_variant Intron 1 of 8 4 ENSP00000462159.2 O15353J3KRT9

Frequencies

GnomAD3 genomes
AF:
0.00332
AC:
478
AN:
144186
Hom.:
4
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00838
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00217
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000628
Gnomad SAS
AF:
0.00293
Gnomad FIN
AF:
0.00135
Gnomad MID
AF:
0.00321
Gnomad NFE
AF:
0.00150
Gnomad OTH
AF:
0.00101
GnomAD4 exome
AF:
0.000882
AC:
446
AN:
505896
Hom.:
1
AF XY:
0.000908
AC XY:
247
AN XY:
272026
show subpopulations
Gnomad4 AFR exome
AF:
0.00507
Gnomad4 AMR exome
AF:
0.000713
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000713
Gnomad4 SAS exome
AF:
0.00144
Gnomad4 FIN exome
AF:
0.00121
Gnomad4 NFE exome
AF:
0.000612
Gnomad4 OTH exome
AF:
0.000965
GnomAD4 genome
AF:
0.00332
AC:
479
AN:
144284
Hom.:
4
Cov.:
0
AF XY:
0.00338
AC XY:
236
AN XY:
69918
show subpopulations
Gnomad4 AFR
AF:
0.00843
Gnomad4 AMR
AF:
0.00209
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000629
Gnomad4 SAS
AF:
0.00270
Gnomad4 FIN
AF:
0.00135
Gnomad4 NFE
AF:
0.00150
Gnomad4 OTH
AF:
0.00100

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10527420; hg19: chr17-26850810; API