17-28523792-TTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TTCTCTCTCTCTCTCTCTC

Variant names:

• chr17-28523792-TTCTCTCTCTC-T
• rs10527420
• NM_001369369.1:c.-14-133_-14-124delTCTCTCTCTC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001369369.1(FOXN1):​c.-14-133_-14-124delTCTCTCTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 644,526 control chromosomes in the GnomAD database, including 15 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0071 (13 hom., cov: 0)
  • Exomes 𝑓: 0.017 (2 hom.)
• Consequence: FOXN1 NM_001369369.1 intron
• 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]

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXN1	NM_001369369.1	c.-14-133_-14-124delTCTCTCTCTC		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_-14-154delTCTCTCTCTC		intron_variant	Intron 1 of 8	1	NM_001369369.1	ENSP00000464645.1
RSKR	ENST00000481916.6	n.*1196-67693_*1196-67684delGAGAGAGAGA		intron_variant	Intron 7 of 7	1		ENSP00000436369.2
FOXN1	ENST00000577936.2	c.-9-168_-9-159delTCTCTCTCTC		intron_variant	Intron 1 of 8	4		ENSP00000462159.2
FOXN1	ENST00000226247.2	c.-177_-168delTCTCTCTCTC		upstream_gene_variant		1		ENSP00000226247.2

Frequencies

GnomAD3 genomes AF: 0.00710 AC: 1024 AN: 144160 Hom.: 13 Cov.: 0

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00391

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000628

Gnomad SAS AF: 0.00112

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000973

Gnomad OTH AF: 0.00760

GnomAD4 exome AF: 0.0174 AC: 8724 AN: 500266 Hom.: 2 AF XY: 0.0173 AC XY: 4660 AN XY: 269038

Gnomad4 AFR exome AF: 0.0613

Gnomad4 AMR exome AF: 0.0112

Gnomad4 ASJ exome AF: 0.0206

Gnomad4 EAS exome AF: 0.00763

Gnomad4 SAS exome AF: 0.0156

Gnomad4 FIN exome AF: 0.0180

Gnomad4 NFE exome AF: 0.0168

Gnomad4 OTH exome AF: 0.0197

GnomAD4 genome AF: 0.00713 AC: 1029 AN: 144260 Hom.: 13 Cov.: 0 AF XY: 0.00741 AC XY: 518 AN XY: 69902

Gnomad4 AFR AF: 0.0232

Gnomad4 AMR AF: 0.00391

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000629

Gnomad4 SAS AF: 0.00113

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.000974

Gnomad4 OTH AF: 0.00752

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10527420; hg19: chr17-26850810;