7-5480548-ATTTTTTTTTTTTTTTTTTT-ATTTTTT
Variant summary
Our verdict is . The variant received 0 ACMG points: 0P and 0B.
Uncertain significance
The NM_024963.6(FBXL18):c.*1214_*1226delAAAAAAAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.076 ( 19 hom., cov: 0)
Failed GnomAD Quality Control
Consequence
FBXL18
NM_024963.6 3_prime_UTR
NM_024963.6 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.548
Publications
0 publications found
Genes affected
FBXL18 (HGNC:21874): (F-box and leucine rich repeat protein 18) The protein encoded by this gene is a member of a family of proteins that contain an approximately 40-amino acid F-box motif. This motif is important for interaction with SKP1 and for targeting some proteins for degradation. The encoded protein has been shown to control the cellular level of FBXL7, a protein that induces mitotic arrest, by targeting it for polyubiquitylation and proteasomal degradation. Members of the F-box protein family, such as FBXL18, are characterized by an approximately 40-amino acid F-box motif. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains. [provided by RefSeq, Mar 2016]
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new If you want to explore the variant's impact on the transcript NM_024963.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_024963.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FBXL18 | MANE Select | c.*1214_*1226delAAAAAAAAAAAAA | 3_prime_UTR | Exon 5 of 5 | NP_079239.3 | ||||
| FBXL18 | c.*1214_*1226delAAAAAAAAAAAAA | 3_prime_UTR | Exon 5 of 5 | NP_001354709.1 | |||||
| FBXL18 | c.*1214_*1226delAAAAAAAAAAAAA | 3_prime_UTR | Exon 5 of 5 | NP_001354710.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FBXL18 | TSL:5 MANE Select | c.*1214_*1226delAAAAAAAAAAAAA | 3_prime_UTR | Exon 5 of 5 | ENSP00000371805.3 | Q96ME1-4 | |||
| FBXL18 | c.*1214_*1226delAAAAAAAAAAAAA | splice_region | Exon 4 of 4 | ENSP00000618927.1 | |||||
| FBXL18 | c.*1214_*1226delAAAAAAAAAAAAA | 3_prime_UTR | Exon 4 of 4 | ENSP00000618927.1 |
Frequencies
GnomAD3 genomes 0.0755 AC: 2928AN: 38766Hom.: 19 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
2928
AN:
38766
Hom.:
Cov.:
0
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 0.0756 AC: 2930AN: 38756Hom.: 19 Cov.: 0 AF XY: 0.0756 AC XY: 1313AN XY: 17366 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
2930
AN:
38756
Hom.:
Cov.:
0
AF XY:
AC XY:
1313
AN XY:
17366
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
421
AN:
10200
American (AMR)
AF:
AC:
166
AN:
2622
Ashkenazi Jewish (ASJ)
AF:
AC:
110
AN:
1206
East Asian (EAS)
AF:
AC:
249
AN:
1784
South Asian (SAS)
AF:
AC:
49
AN:
1132
European-Finnish (FIN)
AF:
AC:
61
AN:
918
Middle Eastern (MID)
AF:
AC:
8
AN:
58
European-Non Finnish (NFE)
AF:
AC:
1810
AN:
20046
Other (OTH)
AF:
AC:
43
AN:
520
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.347
Heterozygous variant carriers
0
161
322
483
644
805
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
34
68
102
136
170
<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:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
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Other links and lift over
dbSNP: rs1180980635 ;
hg19: chr7-5520179;