Variant 22-32474782-C-T 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 ENST00000420700.5(FBXO7):n.-221C>T 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 0.431 in 535,918 control chromosomes in the GnomAD database, including 53,035 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 17762 hom., cov: 32)

Exomes 𝑓: 0.42 ( 35273 hom. )

Consequence

FBXO7
ENST00000420700.5 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.915

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:

(HGNC:):

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=-0.5).

BP6

Variant 22-32474782-C-T is Benign according to our data. Variant chr22-32474782-C-T is described in ClinVar as [Benign]. Clinvar id is 341299.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.32474782C>T		intergenic_region
FBXO7	NM_012179.4 linkuse as main transcript	c.-221C>T		upstream_gene_variant		ENST00000266087.12	NP_036311.3	Q9Y3I1-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
FBXO7	ENST00000420700.5 linkuse as main transcript	n.-221C>T	non_coding_transcript_exon_variant	1/8	5		ENSP00000406155.1	F8WBR0
FBXO7	ENST00000420700.5 linkuse as main transcript	n.-221C>T	5_prime_UTR_variant	1/8	5		ENSP00000406155.1	F8WBR0
FBXO7	ENST00000266087.12 linkuse as main transcript	c.-221C>T	upstream_gene_variant		1	NM_012179.4	ENSP00000266087.7	Q9Y3I1-1
FBXO7	ENST00000425028.5 linkuse as main transcript	n.-221C>T	upstream_gene_variant		5		ENSP00000395823.1	F8WDR9

Frequencies

GnomAD3 genomes

AF:

0.468

AC:

71085

AN:

151816

Hom.:

17724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.628

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.458

Gnomad ASJ

AF:

0.389

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.485

Gnomad MID

AF:

0.452

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.424

GnomAD4 exome

AF:

0.416

AC:

159742

AN:

383984

Hom.:

35273

Cov.:

AF XY:

0.420

AC XY:

84776

AN XY:

201770

show subpopulations

Gnomad4 AFR exome

AF:

0.633

Gnomad4 AMR exome

AF:

0.502

Gnomad4 ASJ exome

AF:

0.381

Gnomad4 EAS exome

AF:

0.654

Gnomad4 SAS exome

AF:

0.509

Gnomad4 FIN exome

AF:

0.444

Gnomad4 NFE exome

AF:

0.365

Gnomad4 OTH exome

AF:

0.427

GnomAD4 genome

AF:

0.468

AC:

71174

AN:

151934

Hom.:

17762

Cov.:

AF XY:

0.475

AC XY:

35249

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.628

Gnomad4 AMR

AF:

0.459

Gnomad4 ASJ

AF:

0.389

Gnomad4 EAS

AF:

0.613

Gnomad4 SAS

AF:

0.495

Gnomad4 FIN

AF:

0.485

Gnomad4 NFE

AF:

0.365

Gnomad4 OTH

AF:

0.429

Alfa

AF:

0.406

Hom.:

1600

Bravo

AF:

0.474

Asia WGS

AF:

0.598

AC:

2077

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2018	- -

Parkinson Disease, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

6.5

DANN

Benign

0.95

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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