8-123503614-G-A

Position:

• chr8-123503614-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_058229.4(FBXO32):​c.979-152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 607,540 control chromosomes in the GnomAD database, including 5,540 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.16 (2886 hom., cov: 32)
  • Exomes 𝑓: 0.088 (2654 hom.)
• Consequence: FBXO32 NM_058229.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.45

Genes affected

FBXO32 (HGNC:16731): (F-box protein 32) 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 contains an F-box domain. This protein is highly expressed during muscle atrophy, whereas mice deficient in this gene were found to be resistant to atrophy. This protein is thus a potential drug target for the treatment of muscle atrophy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jun 2011]

FBXO32 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BP6: Variant 8-123503614-G-A is Benign according to our data. Variant chr8-123503614-G-A is described in ClinVar as [Benign]. Clinvar id is 1222497.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBXO32	NM_058229.4	c.979-152C>T		intron_variant		ENST00000517956.5	NP_478136.1
FBXO32	NM_001242463.2	c.700-152C>T		intron_variant			NP_001229392.1
FBXO32	NM_148177.3	c.544-152C>T		intron_variant			NP_680482.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBXO32	ENST00000517956.5	c.979-152C>T		intron_variant		1	NM_058229.4	ENSP00000428205.1
FBXO32	ENST00000443022.2	c.700-152C>T		intron_variant		1		ENSP00000390790.2
FBXO32	ENST00000287396.2	n.853-152C>T		intron_variant		1
FBXO32	ENST00000524000.5	n.379-152C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23726 AN: 151976 Hom.: 2879 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.144

GnomAD4 exome AF: 0.0885 AC: 40296 AN: 455446 Hom.: 2654 AF XY: 0.0891 AC XY: 21376 AN XY: 240042

Gnomad4 AFR exome AF: 0.337

Gnomad4 AMR exome AF: 0.166

Gnomad4 ASJ exome AF: 0.0608

Gnomad4 EAS exome AF: 0.157

Gnomad4 SAS exome AF: 0.105

Gnomad4 FIN exome AF: 0.0458

Gnomad4 NFE exome AF: 0.0669

Gnomad4 OTH exome AF: 0.107

GnomAD4 genome AF: 0.156 AC: 23771 AN: 152094 Hom.: 2886 Cov.: 32 AF XY: 0.156 AC XY: 11592 AN XY: 74370

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0888 Hom.: 1119

Bravo AF: 0.172

Asia WGS AF: 0.161 AC: 560 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.42
DANN	Benign	0.54

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

Other links and lift over

dbSNP: rs4870855; hg19: chr8-124515854;