11-128693941-CGAGAGAGAGA-C

Variant summary

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

The ENST00000281428.12(FLI1):c.-644_-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 0.0725 in 174,890 control chromosomes in the GnomAD database, including 210 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.076 (205 hom., cov: 0)
  • Exomes 𝑓: 0.069 (5 hom.)
• Consequence: FLI1 ENST00000281428.12 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.85

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-CGAGAGAGAGA-C is Benign according to our data. Variant chr11-128693941-CGAGAGAGAGA-C is described in ClinVar as [Benign]. Clinvar id is 1276147.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SENCR	NR_038908.1	n.112-560_112-551del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SENCR	ENST00000526269.2	n.112-560_112-551del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0760 AC: 6289 AN: 82696 Hom.: 206 Cov.: 0

Gnomad AFR AF: 0.0778

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0917

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0992

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0286

Gnomad NFE AF: 0.0666

Gnomad OTH AF: 0.0630

GnomAD4 exome AF: 0.0693 AC: 6384 AN: 92170 Hom.: 5 AF XY: 0.0683 AC XY: 2988 AN XY: 43768

Gnomad4 AFR exome AF: 0.0861

Gnomad4 AMR exome AF: 0.0839

Gnomad4 ASJ exome AF: 0.0439

Gnomad4 EAS exome AF: 0.129

Gnomad4 SAS exome AF: 0.0507

Gnomad4 FIN exome AF: 0.0996

Gnomad4 NFE exome AF: 0.0581

Gnomad4 OTH exome AF: 0.0646

GnomAD4 genome AF: 0.0760 AC: 6289 AN: 82720 Hom.: 205 Cov.: 0 AF XY: 0.0795 AC XY: 3032 AN XY: 38128

Gnomad4 AFR AF: 0.0779

Gnomad4 AMR AF: 0.0917

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.0980

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0666

Gnomad4 OTH AF: 0.0640

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 18, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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;