rs286784
Variant names:
Your query was ambiguous. Multiple possible variants found:
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
NM_001163315.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.612
Publications
0 publications found
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]
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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 |
---|---|---|---|---|---|---|---|---|
FBXL17 | NM_001163315.3 | c.1746-62470C>T | intron_variant | Intron 6 of 8 | ENST00000542267.7 | NP_001156787.2 | ||
FBXL17 | XM_005272048.5 | c.1746-62470C>T | intron_variant | Intron 6 of 7 | XP_005272105.1 | |||
FBXL17 | XM_011543574.4 | c.1746-62470C>T | intron_variant | Intron 6 of 7 | XP_011541876.1 | |||
FBXL17 | XM_011543575.3 | c.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 |
---|---|---|---|---|---|---|---|---|---|---|
FBXL17 | ENST00000542267.7 | c.1746-62470C>T | intron_variant | Intron 6 of 8 | 1 | NM_001163315.3 | ENSP00000437464.2 | |||
FBXL17 | ENST00000496714.2 | c.753-62470C>T | intron_variant | Intron 5 of 6 | 1 | ENSP00000418111.2 | ||||
FBXL17 | ENST00000481160.1 | n.402-62470C>T | intron_variant | Intron 4 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0433 AC: 6587AN: 152068Hom.: 490 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
6587
AN:
152068
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0433 AC: 6593AN: 152186Hom.: 489 Cov.: 32 AF XY: 0.0413 AC XY: 3073AN XY: 74408 show subpopulations
GnomAD4 genome
AF:
AC:
6593
AN:
152186
Hom.:
Cov.:
32
AF XY:
AC XY:
3073
AN XY:
74408
show subpopulations
African (AFR)
AF:
AC:
6185
AN:
41480
American (AMR)
AF:
AC:
282
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5180
South Asian (SAS)
AF:
AC:
2
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10600
Middle Eastern (MID)
AF:
AC:
4
AN:
294
European-Non Finnish (NFE)
AF:
AC:
42
AN:
68018
Other (OTH)
AF:
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
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
33
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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