rs8086078

Variant names:

• chr18-74132341-G-C
• rs8086078
• NM_001142958.2:c.333-1683C>G

Your query was ambiguous. Multiple possible variants found:

• chr18-74132341-G-C
• chr18-74132341-G-T

Variant summary

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

The NM_001142958.2(FBXO15):​c.333-1683C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 152,106 control chromosomes in the GnomAD database, including 1,501 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 0.098 (1501 hom., cov: 33)
• Consequence: FBXO15 NM_001142958.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

FBXO15 (HGNC:13617): (F-box protein 15) Members of the F-box protein family, such as FBXO15, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBXO15	NM_001142958.2	c.333-1683C>G		intron_variant	Intron 3 of 9	ENST00000419743.7	NP_001136430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBXO15	ENST00000419743.7	c.333-1683C>G		intron_variant	Intron 3 of 9	2	NM_001142958.2	ENSP00000393154.2

Frequencies

GnomAD3 genomes AF: 0.0976 AC: 14841 AN: 151988 Hom.: 1501 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0590

Gnomad FIN AF: 0.00509

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0319

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.0977 AC: 14868 AN: 152106 Hom.: 1501 Cov.: 33 AF XY: 0.0964 AC XY: 7171 AN XY: 74360

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.0604

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.0590

Gnomad4 FIN AF: 0.00509

Gnomad4 NFE AF: 0.0319

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.00587 Hom.: 2

Bravo AF: 0.109

Asia WGS AF: 0.109 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.68

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: rs8086078; hg19: chr18-71799576;