dbSNP rs4904509: FOXN3:c.*94A>G (chr14-89125050-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000557572.1(FOXN3):c.*94A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 429,346 control chromosomes in the GnomAD database, including 100,190 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 0.71 ( 39024 hom., cov: 33)

Exomes 𝑓: 0.66 ( 61166 hom. )

Consequence

FOXN3
ENST00000557572.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

Publications

11 publications found

Variant links:

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]

FOXN3 links:

LOC124903357 (HGNC:):

LOC124903357 links:

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new If you want to explore the variant's impact on the transcript ENST00000557572.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 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.*94A>G		3_prime_UTR	Exon 3 of 3	ENSP00000450783.1	H0YJ43

Frequencies

GnomAD3 genomes

AF:

0.706

AC:

107432

AN:

152076

Hom.:

38958

Cov.:

show subpopulations

Gnomad AFR

AF:

0.862

Gnomad AMI

AF:

0.696

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.652

Gnomad EAS

AF:

0.780

Gnomad SAS

AF:

0.716

Gnomad FIN

AF:

0.522

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.639

Gnomad OTH

AF:

0.696

GnomAD4 exome

AF:

0.661

AC:

183070

AN:

277152

Hom.:

61166

Cov.:

AF XY:

0.663

AC XY:

104457

AN XY:

157580

show subpopulations

African (AFR)

AF:

0.864

AC:

6471

AN:

7490

American (AMR)

AF:

0.659

AC:

14922

AN:

22638

Ashkenazi Jewish (ASJ)

AF:

0.659

AC:

6070

AN:

9216

East Asian (EAS)

AF:

0.778

AC:

7031

AN:

9032

South Asian (SAS)

AF:

0.694

AC:

38138

AN:

54966

European-Finnish (FIN)

AF:

0.538

AC:

6310

AN:

11720

Middle Eastern (MID)

AF:

0.708

AC:

837

AN:

1182

European-Non Finnish (NFE)

AF:

0.639

AC:

94515

AN:

147930

Other (OTH)

AF:

0.676

AC:

8776

AN:

12978

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

3265

6529

9794

13058

16323

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

534

1068

1602

2136

2670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.707

AC:

107557

AN:

152194

Hom.:

39024

Cov.:

AF XY:

0.702

AC XY:

52217

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.862

AC:

35812

AN:

41538

American (AMR)

AF:

0.700

AC:

10714

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.652

AC:

2261

AN:

3468

East Asian (EAS)

AF:

0.781

AC:

4047

AN:

5182

South Asian (SAS)

AF:

0.716

AC:

3454

AN:

4824

European-Finnish (FIN)

AF:

0.522

AC:

5521

AN:

10574

Middle Eastern (MID)

AF:

0.697

AC:

205

AN:

294

European-Non Finnish (NFE)

AF:

0.639

AC:

43432

AN:

67996

Other (OTH)

AF:

0.700

AC:

1476

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1563

3127

4690

6254

7817

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

822

1644

2466

3288

4110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.670

Hom.:

105289

Bravo

AF:

0.726

Asia WGS

AF:

0.757

AC:

2633

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.72

(source)

DANN

Benign

0.42

PhyloP100

-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over