GeneBe

rs738982

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_012179.4(FBXO7):​c.872-75T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FBXO7
NM_012179.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0320

Publications

9 publications found
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 Gene-Disease associations (from GenCC):
  • parkinsonian-pyramidal syndrome
    Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Genomics England PanelApp

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012179.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FBXO7
NM_012179.4
MANE Select
c.872-75T>A
intron
N/ANP_036311.3
FBXO7
NM_001033024.2
c.635-75T>A
intron
N/ANP_001028196.1
FBXO7
NM_001257990.2
c.530-75T>A
intron
N/ANP_001244919.1

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FBXO7
ENST00000266087.12
TSL:1 MANE Select
c.872-75T>A
intron
N/AENSP00000266087.7
FBXO7
ENST00000484607.1
TSL:1
n.542-75T>A
intron
N/A
FBXO7
ENST00000492535.1
TSL:5
n.3890T>A
non_coding_transcript_exon
Exon 5 of 7

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
825838
Hom.:
0
Cov.:
11
AF XY:
0.00
AC XY:
0
AN XY:
435494
African (AFR)
AF:
0.00
AC:
0
AN:
20772
American (AMR)
AF:
0.00
AC:
0
AN:
41824
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
21768
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36584
South Asian (SAS)
AF:
0.00
AC:
0
AN:
71760
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
50278
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4090
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
539462
Other (OTH)
AF:
0.00
AC:
0
AN:
39300
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
5.0
DANN
Benign
0.60
PhyloP100
-0.032

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

Other links and lift over

dbSNP: rs738982; hg19: chr22-32886998; API