rs288139

Variant summary

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

The NM_001163315.3(FBXL17):​c.1746-43803C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,030 control chromosomes in the GnomAD database, including 3,448 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 0.20 ( 3448 hom., cov: 32)

Consequence

FBXL17
NM_001163315.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.194
Variant links:
Genes affected
FBXL17 (HGNC:13615): (F-box and leucine rich repeat protein 17) Members of the F-box protein family, such as FBXL17, 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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FBXL17NM_001163315.3 linkuse as main transcriptc.1746-43803C>T intron_variant ENST00000542267.7
FBXL17XM_005272048.5 linkuse as main transcriptc.1746-43803C>T intron_variant
FBXL17XM_011543574.4 linkuse as main transcriptc.1746-43803C>T intron_variant
FBXL17XM_011543575.3 linkuse as main transcriptc.1746-43803C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FBXL17ENST00000542267.7 linkuse as main transcriptc.1746-43803C>T intron_variant 1 NM_001163315.3 P1Q9UF56-1
FBXL17ENST00000496714.2 linkuse as main transcriptc.754-43803C>T intron_variant 1
FBXL17ENST00000481160.1 linkuse as main transcriptn.402-43803C>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.201
AC:
30497
AN:
151912
Hom.:
3453
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.128
Gnomad AMI
AF:
0.169
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.194
Gnomad EAS
AF:
0.363
Gnomad SAS
AF:
0.468
Gnomad FIN
AF:
0.262
Gnomad MID
AF:
0.187
Gnomad NFE
AF:
0.219
Gnomad OTH
AF:
0.190
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.201
AC:
30503
AN:
152030
Hom.:
3448
Cov.:
32
AF XY:
0.208
AC XY:
15442
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.128
Gnomad4 AMR
AF:
0.139
Gnomad4 ASJ
AF:
0.194
Gnomad4 EAS
AF:
0.364
Gnomad4 SAS
AF:
0.468
Gnomad4 FIN
AF:
0.262
Gnomad4 NFE
AF:
0.219
Gnomad4 OTH
AF:
0.188
Alfa
AF:
0.225
Hom.:
2097
Bravo
AF:
0.184
Asia WGS
AF:
0.380
AC:
1315
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
5.2
DANN
Benign
0.63

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: rs288139; hg19: chr5-107400505; API