17-28523792-TTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TTCTCTCTCTCTCTCTCTCTCTCTCTC

Variant names:

• chr17-28523792-TTC-T
• rs10527420
• NM_001369369.1:c.-14-125_-14-124delTC

Variant summary

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

The NM_001369369.1(FOXN1):​c.-14-125_-14-124delTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 648,298 control chromosomes in the GnomAD database, including 133 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.025 (132 hom., cov: 0)
  • Exomes 𝑓: 0.0087 (1 hom.)
• Consequence: FOXN1 NM_001369369.1 intron
• 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]

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: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXN1	NM_001369369.1	c.-14-125_-14-124delTC		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_-14-162delTC		intron_variant	Intron 1 of 8	1	NM_001369369.1	ENSP00000464645.1
RSKR	ENST00000481916.6	n.*1196-67685_*1196-67684delGA		intron_variant	Intron 7 of 7	1		ENSP00000436369.2
FOXN1	ENST00000577936.2	c.-9-168_-9-167delTC		intron_variant	Intron 1 of 8	4		ENSP00000462159.2

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3626 AN: 144076 Hom.: 132 Cov.: 0

Gnomad AFR AF: 0.0832

Gnomad AMI AF: 0.00449

Gnomad AMR AF: 0.0108

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000209

Gnomad SAS AF: 0.00112

Gnomad FIN AF: 0.00134

Gnomad MID AF: 0.00962

Gnomad NFE AF: 0.00421

Gnomad OTH AF: 0.0228

GnomAD4 exome AF: 0.00872 AC: 4395 AN: 504124 Hom.: 1 AF XY: 0.00881 AC XY: 2389 AN XY: 271022

Gnomad4 AFR exome AF: 0.0685

Gnomad4 AMR exome AF: 0.00725

Gnomad4 ASJ exome AF: 0.00319

Gnomad4 EAS exome AF: 0.00107

Gnomad4 SAS exome AF: 0.0125

Gnomad4 FIN exome AF: 0.00228

Gnomad4 NFE exome AF: 0.00702

Gnomad4 OTH exome AF: 0.0104

GnomAD4 genome AF: 0.0252 AC: 3632 AN: 144174 Hom.: 132 Cov.: 0 AF XY: 0.0240 AC XY: 1674 AN XY: 69866

Gnomad4 AFR AF: 0.0832

Gnomad4 AMR AF: 0.0108

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000210

Gnomad4 SAS AF: 0.00113

Gnomad4 FIN AF: 0.00134

Gnomad4 NFE AF: 0.00421

Gnomad4 OTH AF: 0.0226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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;