rs286784
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000542267.7(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
ENST00000542267.7 intron
ENST00000542267.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.612
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 made for transcript
Verdict is Benign. Variant got -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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBXL17 | NM_001163315.3 | c.1746-62470C>T | intron_variant | ENST00000542267.7 | NP_001156787.2 | |||
FBXL17 | XM_005272048.5 | c.1746-62470C>T | intron_variant | XP_005272105.1 | ||||
FBXL17 | XM_011543574.4 | c.1746-62470C>T | intron_variant | XP_011541876.1 | ||||
FBXL17 | XM_011543575.3 | c.1746-62470C>T | intron_variant | XP_011541877.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBXL17 | ENST00000542267.7 | c.1746-62470C>T | intron_variant | 1 | NM_001163315.3 | ENSP00000437464 | P1 | |||
FBXL17 | ENST00000496714.2 | c.754-62470C>T | intron_variant | 1 | ENSP00000418111 | |||||
FBXL17 | ENST00000481160.1 | n.402-62470C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0433 AC: 6587AN: 152068Hom.: 490 Cov.: 32
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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
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at