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GeneBe

rs7130622

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002017.5(FLI1):c.*628A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0293 in 214,520 control chromosomes in the GnomAD database, including 365 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 0.038 ( 342 hom., cov: 32)
Exomes 𝑓: 0.0071 ( 23 hom. )

Consequence

FLI1
NM_002017.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.53
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]

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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=-0.48).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FLI1NM_002017.5 linkuse as main transcriptc.*628A>C 3_prime_UTR_variant 9/9 ENST00000527786.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FLI1ENST00000527786.7 linkuse as main transcriptc.*628A>C 3_prime_UTR_variant 9/91 NM_002017.5 P1Q01543-1

Frequencies

GnomAD3 genomes
AF:
0.0382
AC:
5818
AN:
152148
Hom.:
340
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.132
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0171
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000750
Gnomad OTH
AF:
0.0263
GnomAD4 exome
AF:
0.00707
AC:
440
AN:
62254
Hom.:
23
Cov.:
0
AF XY:
0.00647
AC XY:
187
AN XY:
28894
show subpopulations
Gnomad4 AFR exome
AF:
0.114
Gnomad4 AMR exome
AF:
0.0121
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000813
Gnomad4 OTH exome
AF:
0.0152
GnomAD4 genome
AF:
0.0384
AC:
5840
AN:
152266
Hom.:
342
Cov.:
32
AF XY:
0.0374
AC XY:
2782
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.132
Gnomad4 AMR
AF:
0.0171
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000828
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000750
Gnomad4 OTH
AF:
0.0260
Alfa
AF:
0.0115
Hom.:
83
Bravo
AF:
0.0436
Asia WGS
AF:
0.00808
AC:
28
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
11
Dann
Benign
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7130622; hg19: chr11-128681511; API