9-37518257-G-C
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_012166.3(FBXO10):āc.2382C>Gā(p.Leu794=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0011 in 1,614,072 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0060 ( 8 hom., cov: 33)
Exomes š: 0.00059 ( 9 hom. )
Consequence
FBXO10
NM_012166.3 synonymous
NM_012166.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0320
Genes affected
FBXO10 (HGNC:13589): (F-box protein 10) Members of the F-box protein family, such as FBXO10, 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 -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
Variant 9-37518257-G-C is Benign according to our data. Variant chr9-37518257-G-C is described in ClinVar as [Benign]. Clinvar id is 786908.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.032 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00601 (915/152364) while in subpopulation AFR AF= 0.0211 (876/41588). AF 95% confidence interval is 0.0199. There are 8 homozygotes in gnomad4. There are 425 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBXO10 | NM_012166.3 | c.2382C>G | p.Leu794= | synonymous_variant | 9/11 | ENST00000432825.7 | NP_036298.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBXO10 | ENST00000432825.7 | c.2382C>G | p.Leu794= | synonymous_variant | 9/11 | 1 | NM_012166.3 | ENSP00000403802 | P1 | |
FBXO10 | ENST00000276960.7 | c.*589C>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/9 | 5 | ENSP00000276960 |
Frequencies
GnomAD3 genomes AF: 0.00600 AC: 914AN: 152246Hom.: 8 Cov.: 33
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GnomAD3 exomes AF: 0.00138 AC: 345AN: 249296Hom.: 2 AF XY: 0.00105 AC XY: 142AN XY: 135242
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GnomAD4 exome AF: 0.000593 AC: 867AN: 1461708Hom.: 9 Cov.: 32 AF XY: 0.000507 AC XY: 369AN XY: 727136
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GnomAD4 genome AF: 0.00601 AC: 915AN: 152364Hom.: 8 Cov.: 33 AF XY: 0.00570 AC XY: 425AN XY: 74512
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 04, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at