11-128693941-CGAGA-C

Position:

• chr11-128693941-CGAGA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000281428.12(FLI1):​c.-638_-635del 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.710

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)

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SENCR	NR_038908.1	n.112-554_112-551del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SENCR	ENST00000526269.2	n.112-554_112-551del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 4921 AN: 82514 Hom.: 137 Cov.: 0

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.0618

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.0632

Gnomad MID AF: 0.0571

Gnomad NFE AF: 0.0508

Gnomad OTH AF: 0.0536

GnomAD4 exome AF: 0.0727 AC: 6523 AN: 89714 Hom.: 2 AF XY: 0.0701 AC XY: 2987 AN XY: 42610

Gnomad4 AFR exome AF: 0.0904

Gnomad4 AMR exome AF: 0.120

Gnomad4 ASJ exome AF: 0.0758

Gnomad4 EAS exome AF: 0.0691

Gnomad4 SAS exome AF: 0.0269

Gnomad4 FIN exome AF: 0.0360

Gnomad4 NFE exome AF: 0.0719

Gnomad4 OTH exome AF: 0.0784

GnomAD4 genome AF: 0.0596 AC: 4920 AN: 82536 Hom.: 136 Cov.: 0 AF XY: 0.0610 AC XY: 2321 AN XY: 38030

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.0417

Gnomad4 FIN AF: 0.0632

Gnomad4 NFE AF: 0.0508

Gnomad4 OTH AF: 0.0531

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs57930585; hg19: chr11-128563836;