18-74107551-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001142958.2(FBXO15):​c.1138+15817C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,900 control chromosomes in the GnomAD database, including 7,814 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 0.26 ( 7814 hom., cov: 32)

Consequence

FBXO15
NM_001142958.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.753
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FBXO15NM_001142958.2 linkc.1138+15817C>A intron_variant Intron 8 of 9 ENST00000419743.7 NP_001136430.1 Q8NCQ5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FBXO15ENST00000419743.7 linkc.1138+15817C>A intron_variant Intron 8 of 9 2 NM_001142958.2 ENSP00000393154.2 Q8NCQ5-1

Frequencies

GnomAD3 genomes
AF:
0.264
AC:
40024
AN:
151782
Hom.:
7780
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.537
Gnomad AMI
AF:
0.138
Gnomad AMR
AF:
0.296
Gnomad ASJ
AF:
0.158
Gnomad EAS
AF:
0.273
Gnomad SAS
AF:
0.135
Gnomad FIN
AF:
0.0706
Gnomad MID
AF:
0.218
Gnomad NFE
AF:
0.137
Gnomad OTH
AF:
0.239
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.264
AC:
40112
AN:
151900
Hom.:
7814
Cov.:
32
AF XY:
0.263
AC XY:
19505
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.538
Gnomad4 AMR
AF:
0.296
Gnomad4 ASJ
AF:
0.158
Gnomad4 EAS
AF:
0.272
Gnomad4 SAS
AF:
0.135
Gnomad4 FIN
AF:
0.0706
Gnomad4 NFE
AF:
0.137
Gnomad4 OTH
AF:
0.237
Alfa
AF:
0.131
Hom.:
824
Bravo
AF:
0.298
Asia WGS
AF:
0.233
AC:
811
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.30
DANN
Benign
0.26

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.

Other links and lift over

dbSNP: rs1113144; hg19: chr18-71774786; API