17-28523792-TTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_001369369.1(FOXN1):​c.-14-131_-14-124dupTCTCTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00506 in 649,048 control chromosomes in the GnomAD database, including 17 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0079 ( 11 hom., cov: 0)
Exomes 𝑓: 0.0043 ( 6 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00786 (1133/144224) while in subpopulation EAS AF= 0.0164 (78/4760). AF 95% confidence interval is 0.0137. There are 11 homozygotes in gnomad4. There are 530 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 11 SD gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FOXN1NM_001369369.1 linkc.-14-131_-14-124dupTCTCTCTC 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_-14-163insTCTCTCTC intron_variant Intron 1 of 8 1 NM_001369369.1 ENSP00000464645.1 O15353
RSKRENST00000481916.6 linkn.*1196-67684_*1196-67683insGAGAGAGA intron_variant Intron 7 of 7 1 ENSP00000436369.2 Q96LW2-2
FOXN1ENST00000577936.2 linkc.-9-169_-9-168insTCTCTCTC intron_variant Intron 1 of 8 4 ENSP00000462159.2 O15353J3KRT9

Frequencies

GnomAD3 genomes
AF:
0.00789
AC:
1137
AN:
144124
Hom.:
11
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0147
Gnomad AMI
AF:
0.0113
Gnomad AMR
AF:
0.00685
Gnomad ASJ
AF:
0.00904
Gnomad EAS
AF:
0.0166
Gnomad SAS
AF:
0.00428
Gnomad FIN
AF:
0.00259
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00470
Gnomad OTH
AF:
0.00457
GnomAD4 exome
AF:
0.00426
AC:
2149
AN:
504824
Hom.:
6
AF XY:
0.00401
AC XY:
1088
AN XY:
271472
show subpopulations
Gnomad4 AFR exome
AF:
0.0105
Gnomad4 AMR exome
AF:
0.00754
Gnomad4 ASJ exome
AF:
0.00394
Gnomad4 EAS exome
AF:
0.0101
Gnomad4 SAS exome
AF:
0.00346
Gnomad4 FIN exome
AF:
0.00401
Gnomad4 NFE exome
AF:
0.00314
Gnomad4 OTH exome
AF:
0.00537
GnomAD4 genome
AF:
0.00786
AC:
1133
AN:
144224
Hom.:
11
Cov.:
0
AF XY:
0.00758
AC XY:
530
AN XY:
69886
show subpopulations
Gnomad4 AFR
AF:
0.0147
Gnomad4 AMR
AF:
0.00670
Gnomad4 ASJ
AF:
0.00904
Gnomad4 EAS
AF:
0.0164
Gnomad4 SAS
AF:
0.00383
Gnomad4 FIN
AF:
0.00259
Gnomad4 NFE
AF:
0.00470
Gnomad4 OTH
AF:
0.00452

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