11-128693941-CGAGA-C
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000281428.12(FLI1):c.-638_-635delGAGA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0664 in 172,250 control chromosomes in the GnomAD database, including 138 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.060 ( 136 hom., cov: 0)
Exomes 𝑓: 0.073 ( 2 hom. )
Consequence
FLI1
ENST00000281428.12 5_prime_UTR
ENST00000281428.12 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.710
Publications
0 publications found
Genes affected
FLI1 (HGNC:3749): (Fli-1 proto-oncogene, ETS transcription factor) This gene encodes a transcription factor containing an ETS DNA-binding domain. The gene can undergo a t(11;22)(q24;q12) translocation with the Ewing sarcoma gene on chromosome 22, which results in a fusion gene that is present in the majority of Ewing sarcoma cases. An acute lymphoblastic leukemia-associated t(4;11)(q21;q23) translocation involving this gene has also been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 11-128693941-CGAGA-C is Benign according to our data. Variant chr11-128693941-CGAGA-C is described in ClinVar as [Benign]. Clinvar id is 1235009.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLI1 | NM_002017.5 | c.-317_-314delGAGA | upstream_gene_variant | ENST00000527786.7 | NP_002008.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0596 AC: 4921AN: 82514Hom.: 137 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
4921
AN:
82514
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:
GnomAD4 exome AF: 0.0727 AC: 6523AN: 89714Hom.: 2 AF XY: 0.0701 AC XY: 2987AN XY: 42610 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
6523
AN:
89714
Hom.:
AF XY:
AC XY:
2987
AN XY:
42610
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
340
AN:
3760
American (AMR)
AF:
AC:
310
AN:
2588
Ashkenazi Jewish (ASJ)
AF:
AC:
388
AN:
5122
East Asian (EAS)
AF:
AC:
767
AN:
11104
South Asian (SAS)
AF:
AC:
47
AN:
1750
European-Finnish (FIN)
AF:
AC:
71
AN:
1974
Middle Eastern (MID)
AF:
AC:
36
AN:
542
European-Non Finnish (NFE)
AF:
AC:
4010
AN:
55808
Other (OTH)
AF:
AC:
554
AN:
7066
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.312
Heterozygous variant carriers
0
426
852
1278
1704
2130
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0596 AC: 4920AN: 82536Hom.: 136 Cov.: 0 AF XY: 0.0610 AC XY: 2321AN XY: 38030 show subpopulations
GnomAD4 genome
AF:
AC:
4920
AN:
82536
Hom.:
Cov.:
0
AF XY:
AC XY:
2321
AN XY:
38030
show subpopulations
African (AFR)
AF:
AC:
1246
AN:
18344
American (AMR)
AF:
AC:
840
AN:
7786
Ashkenazi Jewish (ASJ)
AF:
AC:
108
AN:
2480
East Asian (EAS)
AF:
AC:
94
AN:
2696
South Asian (SAS)
AF:
AC:
88
AN:
2110
European-Finnish (FIN)
AF:
AC:
200
AN:
3166
Middle Eastern (MID)
AF:
AC:
9
AN:
134
European-Non Finnish (NFE)
AF:
AC:
2238
AN:
44086
Other (OTH)
AF:
AC:
62
AN:
1168
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.437
Heterozygous variant carriers
0
158
316
473
631
789
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 20, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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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