rs8006194

Variant names:

• chr14-89444509-C-A
• rs8006194
• ENST00000345097.8:c.-14-32019G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001085471.2(FOXN3):​c.-14-32019G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,594 control chromosomes in the GnomAD database, including 18,777 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 0.49 (18777 hom., cov: 31)
• Consequence: FOXN3 NM_001085471.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

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]

ENSG00000259053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXN3	NM_001085471.2	c.-14-32019G>T		intron_variant	Intron 1 of 6		NP_001078940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXN3	ENST00000345097.8	c.-14-32019G>T		intron_variant	Intron 1 of 6	1		ENSP00000343288.4
FOXN3	ENST00000555353.5	c.-14-32019G>T		intron_variant	Intron 1 of 5	1		ENSP00000452227.1
FOXN3	ENST00000555855.5	c.-14-32019G>T		intron_variant	Intron 2 of 3	5		ENSP00000451135.1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73769 AN: 151486 Hom.: 18763 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.635

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.487 AC: 73806 AN: 151594 Hom.: 18777 Cov.: 31 AF XY: 0.491 AC XY: 36372 AN XY: 74054

African (AFR) AF: 0.342 AC: 14108 AN: 41282

American (AMR) AF: 0.625 AC: 9542 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1860 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2015 AN: 5146

South Asian (SAS) AF: 0.604 AC: 2906 AN: 4810

European-Finnish (FIN) AF: 0.517 AC: 5390 AN: 10420

Middle Eastern (MID) AF: 0.646 AC: 186 AN: 288

European-Non Finnish (NFE) AF: 0.532 AC: 36133 AN: 67904

Other (OTH) AF: 0.535 AC: 1127 AN: 2106

Alfa AF: 0.505 Hom.: 3573

Bravo AF: 0.491

Asia WGS AF: 0.456 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	13
DANN	Benign	0.90
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Publications

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Other links and lift over

dbSNP: rs8006194; hg19: chr14-89910853;