Genetic Variant FBXO2:n.*1387T>A (chr1-11637041-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000642025.1(FBXO2):n.*1387T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,346 control chromosomes in the GnomAD database, including 56,824 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 0.86 ( 56804 hom., cov: 34)

Exomes 𝑓: 0.88 ( 20 hom. )

Consequence

FBXO2
ENST00000642025.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.901

Publications

3 publications found

Variant links:

Genes affected

FBXO2 (HGNC:13581): (F-box protein 2) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of the ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbxs class. This protein is highly similar to the rat NFB42 (neural F Box 42 kDa) protein which is enriched in the nervous system and may play a role in maintaining neurons in a postmitotic state. [provided by RefSeq, Jul 2008]

FBXO2 links:

ENSG00000284708 (HGNC:):

ENSG00000284708 links:

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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=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642025.1. 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

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
FBXO2	ENST00000642025.1	n.*1387T>A	non_coding_transcript_exon	Exon 7 of 7	ENSP00000493057.1	A0A286YF37
FBXO2	ENST00000642025.1	n.*1387T>A	3_prime_UTR	Exon 7 of 7	ENSP00000493057.1	A0A286YF37
ENSG00000284708	ENST00000642131.1	n.54-4335A>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.861

AC:

131014

AN:

152180

Hom.:

56768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.813

Gnomad AMI

AF:

0.924

Gnomad AMR

AF:

0.852

Gnomad ASJ

AF:

0.914

Gnomad EAS

AF:

0.579

Gnomad SAS

AF:

0.852

Gnomad FIN

AF:

0.876

Gnomad MID

AF:

0.921

Gnomad NFE

AF:

0.908

Gnomad OTH

AF:

0.867

GnomAD4 exome

AF:

0.875

AC:

AN:

Hom.:

Cov.:

AF XY:

0.861

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.969

AC:

AN:

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.700

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.861

AC:

131105

AN:

152298

Hom.:

56804

Cov.:

AF XY:

0.858

AC XY:

63919

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.813

AC:

33762

AN:

41536

American (AMR)

AF:

0.852

AC:

13037

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.914

AC:

3173

AN:

3472

East Asian (EAS)

AF:

0.579

AC:

2994

AN:

5174

South Asian (SAS)

AF:

0.852

AC:

4113

AN:

4830

European-Finnish (FIN)

AF:

0.876

AC:

9299

AN:

10614

Middle Eastern (MID)

AF:

0.918

AC:

270

AN:

294

European-Non Finnish (NFE)

AF:

0.908

AC:

61787

AN:

68040

Other (OTH)

AF:

0.863

AC:

1827

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

934

1869

2803

3738

4672

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

892

1784

2676

3568

4460

<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:

0.890

Hom.:

2924

Bravo

AF:

0.853

Asia WGS

AF:

0.736

AC:

2558

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.33

(source)

DANN

Benign

0.49

PhyloP100

-0.90

Splicing

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

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