rs286784

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001163315.3(FBXL17):​c.1746-62470C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 152,186 control chromosomes in the GnomAD database, including 489 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 0.043 ( 489 hom., cov: 32)

Consequence

FBXL17
NM_001163315.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.612

Publications

0 publications found
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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FBXL17NM_001163315.3 linkc.1746-62470C>T intron_variant Intron 6 of 8 ENST00000542267.7 NP_001156787.2 Q9UF56-1
FBXL17XM_005272048.5 linkc.1746-62470C>T intron_variant Intron 6 of 7 XP_005272105.1
FBXL17XM_011543574.4 linkc.1746-62470C>T intron_variant Intron 6 of 7 XP_011541876.1
FBXL17XM_011543575.3 linkc.1746-62470C>T intron_variant Intron 6 of 7 XP_011541877.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FBXL17ENST00000542267.7 linkc.1746-62470C>T intron_variant Intron 6 of 8 1 NM_001163315.3 ENSP00000437464.2 Q9UF56-1
FBXL17ENST00000496714.2 linkc.753-62470C>T intron_variant Intron 5 of 6 1 ENSP00000418111.2 A0A6E1XD66
FBXL17ENST00000481160.1 linkn.402-62470C>T intron_variant Intron 4 of 4 3

Frequencies

GnomAD3 genomes
AF:
0.0433
AC:
6587
AN:
152068
Hom.:
490
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.149
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0185
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.000617
Gnomad OTH
AF:
0.0368
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0433
AC:
6593
AN:
152186
Hom.:
489
Cov.:
32
AF XY:
0.0413
AC XY:
3073
AN XY:
74408
show subpopulations
African (AFR)
AF:
0.149
AC:
6185
AN:
41480
American (AMR)
AF:
0.0184
AC:
282
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.000288
AC:
1
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5180
South Asian (SAS)
AF:
0.000415
AC:
2
AN:
4824
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10600
Middle Eastern (MID)
AF:
0.0136
AC:
4
AN:
294
European-Non Finnish (NFE)
AF:
0.000617
AC:
42
AN:
68018
Other (OTH)
AF:
0.0365
AC:
77
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
282
564
846
1128
1410
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
66
132
198
264
330
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0141
Hom.:
10
Bravo
AF:
0.0497
Asia WGS
AF:
0.00953
AC:
33
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
3.2
DANN
Benign
0.27
PhyloP100
0.61
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs286784; hg19: chr5-107419172; API