rs6851312

chr4-174247002-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012180.3(FBXO8):c.457-5784T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,844 control chromosomes in the GnomAD database, including 7,910 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 0.31 (7910 hom., cov: 32)
• Consequence: FBXO8 NM_012180.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

FBXO8 (HGNC:13587): (F-box protein 8) 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. It contains a C-terminal amino acid sequence that bears a significant similarity with a portion of yeast Sec7p, a critical regulator of vesicular protein transport. This human protein may interact with ADP-ribosylation factor(s)(ARFs) and exhibit ARF-GEF (guanine nucleotide exchange factor) activity. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBXO8	NM_012180.3	c.457-5784T>C		intron_variant		ENST00000393674.7
FBXO8	XR_007096390.1	n.591+2914T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBXO8	ENST00000393674.7	c.457-5784T>C		intron_variant		1	NM_012180.3	P1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47333 AN: 151726 Hom.: 7906 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.325

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.312 AC: 47353 AN: 151844 Hom.: 7910 Cov.: 32 AF XY: 0.307 AC XY: 22756 AN XY: 74218

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.322

Alfa AF: 0.351 Hom.: 19364

Bravo AF: 0.303

Asia WGS AF: 0.132 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.7
Dann	Benign	0.70

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: rs6851312; hg19: chr4-175168153;