GeneBe

rs57930585

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000281428.12(FLI1):​c.-672_-635delGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 93,914 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 0)
Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

FLI1
ENST00000281428.12 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.85

Publications

0 publications found
Variant links:
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]
SENCR (HGNC:44177): (smooth muscle and endothelial cell enriched migration/differentiation-associated lncRNA)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FLI1NM_002017.5 linkc.-317_-280delGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA upstream_gene_variant ENST00000527786.7 NP_002008.2 Q01543-1A0A024R3M5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FLI1ENST00000527786.7 linkc.-317_-280delGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA upstream_gene_variant 1 NM_002017.5 ENSP00000433488.2 Q01543-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.0000106
AC:
1
AN:
93914
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
44586
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
3946
American (AMR)
AF:
0.000363
AC:
1
AN:
2754
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
5370
East Asian (EAS)
AF:
0.00
AC:
0
AN:
11606
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1776
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
1998
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
574
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
58464
Other (OTH)
AF:
0.00
AC:
0
AN:
7426
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs57930585; hg19: chr11-128563836; API