rs236796

Variant summary

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

The NM_001282540.2(FBXW10B):​c.2007-8273T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,006 control chromosomes in the GnomAD database, including 8,002 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 0.22 ( 8002 hom., cov: 29)

Consequence

FBXW10B
NM_001282540.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.943
Variant links:
Genes affected
FBXW10B (HGNC:14379): (F-box and WD repeat domain containing 10B) Members of the F-box protein family, such as FBXW10, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603034), 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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FBXW10BNM_001282540.2 linkc.2007-8273T>C intron_variant NP_001269469.1 Q9BXD7A0A087WSX6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000251537ENST00000455584.2 linkc.2778-3120T>C intron_variant 2 ENSP00000402644.2 H0Y626
FBXW10BENST00000395667.7 linkc.2007-8273T>C intron_variant 5 ENSP00000379026.2 A0A087WSX6

Frequencies

GnomAD3 genomes
AF:
0.218
AC:
33176
AN:
151894
Hom.:
7973
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.569
Gnomad AMI
AF:
0.0417
Gnomad AMR
AF:
0.227
Gnomad ASJ
AF:
0.0510
Gnomad EAS
AF:
0.508
Gnomad SAS
AF:
0.0702
Gnomad FIN
AF:
0.0449
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0321
Gnomad OTH
AF:
0.178
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.219
AC:
33248
AN:
152006
Hom.:
8002
Cov.:
29
AF XY:
0.220
AC XY:
16317
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.570
Gnomad4 AMR
AF:
0.227
Gnomad4 ASJ
AF:
0.0510
Gnomad4 EAS
AF:
0.508
Gnomad4 SAS
AF:
0.0688
Gnomad4 FIN
AF:
0.0449
Gnomad4 NFE
AF:
0.0321
Gnomad4 OTH
AF:
0.181
Alfa
AF:
0.138
Hom.:
537
Bravo
AF:
0.253
Asia WGS
AF:
0.274
AC:
951
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.8
DANN
Benign
0.31

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: rs236796; hg19: chr17-15480617; API