19-38964894-T-C

Position:

• chr19-38964894-T-C

Variant summary

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

The NM_024907.7(FBXO17):​c.-18+10692A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,116 control chromosomes in the GnomAD database, including 45,893 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 0.77 (45893 hom., cov: 31)
• Consequence: FBXO17 NM_024907.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533

Genes affected

FBXO17 (HGNC:18754): (F-box protein 17) This gene encodes a member of the F-box protein family which is characterized by the F-box motif. 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 contains an F-box domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

FBXO17 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBXO17	NM_024907.7	c.-18+10692A>G		intron_variant		ENST00000292852.9	NP_079183.4
FBXO17	NR_104026.2	n.157+10692A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBXO17	ENST00000292852.9	c.-18+10692A>G		intron_variant		1	NM_024907.7	ENSP00000292852.3
FBXO17	ENST00000596025.5	n.-18+10692A>G		intron_variant		2		ENSP00000470101.1

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116649 AN: 151998 Hom.: 45837 Cov.: 31

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.768 AC: 116764 AN: 152116 Hom.: 45893 Cov.: 31 AF XY: 0.773 AC XY: 57463 AN XY: 74368

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.753

Alfa AF: 0.688 Hom.: 75181

Bravo AF: 0.784

Asia WGS AF: 0.874 AC: 3037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.48

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: rs12151188; hg19: chr19-39455534;