11-128759766-C-T

Variant names:

• chr11-128759766-C-T
• rs670809
• NM_002017.5:c.230+1440C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002017.5(FLI1):​c.230+1440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,170 control chromosomes in the GnomAD database, including 41,358 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 0.74 (41358 hom., cov: 32)
• Consequence: FLI1 NM_002017.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLI1	NM_002017.5	c.230+1440C>T		intron_variant	Intron 2 of 8	ENST00000527786.7	NP_002008.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLI1	ENST00000527786.7	c.230+1440C>T		intron_variant	Intron 2 of 8	1	NM_002017.5	ENSP00000433488.2

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111928 AN: 152052 Hom.: 41297 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.736 AC: 112048 AN: 152170 Hom.: 41358 Cov.: 32 AF XY: 0.737 AC XY: 54858 AN XY: 74390

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.722

Alfa AF: 0.692 Hom.: 3009

Bravo AF: 0.739

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.61
DANN	Benign	0.66

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

Other links and lift over

dbSNP: rs670809; hg19: chr11-128629661;