Variant rs8140067 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_012179.4(FBXO7):c.122+331C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,595,388 control chromosomes in the GnomAD database, including 33,331 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 2736 hom., cov: 33)

Exomes 𝑓: 0.20 ( 30595 hom. )

Consequence

FBXO7
NM_012179.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.19

Variant links:

Genes affected

FBXO7 (HGNC:13586): (F-box protein 7) 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 and it may play a role in regulation of hematopoiesis. Alternatively spliced transcript variants of this gene have been identified with the full-length natures of only some variants being determined. [provided by RefSeq, Jul 2008]

FBXO7 links:

FBXO7 (HGNC:):

FBXO7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 22-32475455-C-A is Benign according to our data. Variant chr22-32475455-C-A is described in ClinVar as [Benign]. Clinvar id is 1230871.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
FBXO7	NM_012179.4 linkuse as main transcript	c.122+331C>A	intron_variant	ENST00000266087.12	NP_036311.3	Q9Y3I1-1
FBXO7	NM_001033024.2 linkuse as main transcript	c.37+57C>A	intron_variant		NP_001028196.1	Q9Y3I1-2
FBXO7	NM_001257990.2 linkuse as main transcript	c.-221+57C>A	intron_variant		NP_001244919.1	Q9Y3I1-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBXO7	ENST00000266087.12 linkuse as main transcript	c.122+331C>A		intron_variant		1	NM_012179.4	ENSP00000266087.7		Q9Y3I1-1

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28692

AN:

152068

Hom.:

2732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.131

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.187

GnomAD4 exome

AF:

0.204

AC:

294038

AN:

1443202

Hom.:

30595

Cov.:

AF XY:

0.202

AC XY:

145226

AN XY:

717832

show subpopulations

Gnomad4 AFR exome

AF:

0.140

Gnomad4 AMR exome

AF:

0.199

Gnomad4 ASJ exome

AF:

0.254

Gnomad4 EAS exome

AF:

0.187

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.219

Gnomad4 NFE exome

AF:

0.210

Gnomad4 OTH exome

AF:

0.199

GnomAD4 genome

AF:

0.189

AC:

28711

AN:

152186

Hom.:

2736

Cov.:

AF XY:

0.189

AC XY:

14072

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.145

Gnomad4 AMR

AF:

0.205

Gnomad4 ASJ

AF:

0.256

Gnomad4 EAS

AF:

0.155

Gnomad4 SAS

AF:

0.126

Gnomad4 FIN

AF:

0.236

Gnomad4 NFE

AF:

0.209

Gnomad4 OTH

AF:

0.184

Alfa

AF:

0.194

Hom.:

3148

Bravo

AF:

0.185

Asia WGS

AF:

0.128

AC:

444

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 25, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.029

DANN

Benign

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over