rs7158359

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557572.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXN3	ENST00000557572.1	TSL:3	c.45-2511T>C		intron	N/A	ENSP00000450783.1	H0YJ43

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

African (AFR) AF: 0.417 AC: 17309 AN: 41480

American (AMR) AF: 0.337 AC: 5154 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3472

East Asian (EAS) AF: 0.260 AC: 1348 AN: 5178

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4818

European-Finnish (FIN) AF: 0.137 AC: 1452 AN: 10594

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12211 AN: 67966

Other (OTH) AF: 0.264 AC: 558 AN: 2116

Alfa AF: 0.291 Hom.: 2843

Bravo AF: 0.284

Asia WGS AF: 0.242 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.19
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7158359; hg19: chr14-89594295;