rs7158359

Variant names:

• chr14-89127951-A-G
• rs7158359
• ENST00000557572.1:c.45-2511T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000557572.1(FOXN3):​c.45-2511T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,108 control chromosomes in the GnomAD database, including 6,173 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (6173 hom., cov: 33)
• Consequence: FOXN3 ENST00000557572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

FOXN3 (HGNC:1928): (forkhead box N3) This gene is a member of the forkhead/winged helix transcription factor family. Checkpoints are eukaryotic DNA damage-inducible cell cycle arrests at G1 and G2. Checkpoint suppressor 1 suppresses multiple yeast checkpoint mutations including mec1, rad9, rad53 and dun1 by activating a MEC1-independent checkpoint pathway. Alternative splicing is observed at the locus, resulting in distinct isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXN3	ENST00000557572.1	c.45-2511T>C		intron_variant	Intron 1 of 2	3		ENSP00000450783.1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39961 AN: 151994 Hom.: 6162 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.267

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.263 AC: 40021 AN: 152108 Hom.: 6173 Cov.: 33 AF XY: 0.264 AC XY: 19622 AN XY: 74366

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.264

Alfa AF: 0.227 Hom.: 636

Bravo AF: 0.284

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7158359; hg19: chr14-89594295;