Genetic Variant SENCR:n.112-584_112-551delTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC (chr11-128693941-CGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001440369.1(FLI1):c.-82+817_-82+850delGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA variant causes a intron 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 0.000012 ( 0 hom., cov: 0)

Consequence

FLI1
NM_001440369.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.85

Publications

0 publications found

Variant links:

Genes affected

SENCR (HGNC:44177): (smooth muscle and endothelial cell enriched migration/differentiation-associated lncRNA)

SENCR links:

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]

FLI1 Gene-Disease associations (from GenCC):

bleeding disorder, platelet-type, 21
Inheritance: AR, AD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen

FLI1 links:

Genome browser will be placed here

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_001440369.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
FLI1	NM_001440369.1	c.-82+817_-82+850delGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	intron	N/A	NP_001427298.1
FLI1	NM_001440370.1	c.-82+8588_-82+8621delGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	intron	N/A	NP_001427299.1
FLI1	NM_001440371.1	c.-82+1160_-82+1193delGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	intron	N/A	NP_001427300.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SENCR	ENST00000526269.2	TSL:1	n.112-584_112-551delTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC	intron	N/A
FLI1	ENST00000897157.1		c.-299_-266delGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	5_prime_UTR	Exon 1 of 10	ENSP00000567216.1
FLI1	ENST00000897156.1		c.-299_-266delGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	5_prime_UTR	Exon 1 of 8	ENSP00000567215.1

Frequencies

GnomAD3 genomes

AF:

0.0000121

AC:

AN:

82812

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000226

Gnomad OTH

AF:

0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0000121

AC:

AN:

82836

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

38180

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

18426

American (AMR)

AF:

0.00

AC:

AN:

7832

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2484

East Asian (EAS)

AF:

0.00

AC:

AN:

2702

South Asian (SAS)

AF:

0.00

AC:

AN:

2116

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3184

Middle Eastern (MID)

AF:

0.00

AC:

AN:

134

European-Non Finnish (NFE)

AF:

0.0000226

AC:

AN:

44220

Other (OTH)

AF:

0.00

AC:

AN:

1172

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.775

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.9

Splicing

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

Publications

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11-128693941-CGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-CGAGA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over