11-128693941-CGAGAGAGA-C

Position:

• chr11-128693941-CGAGAGAGA-C

Variant summary

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

The ENST00000281428.12(FLI1):​c.-642_-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 0.0545 in 174,414 control chromosomes in the GnomAD database, including 103 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.041 (101 hom., cov: 0)
  • Exomes 𝑓: 0.067 (2 hom.)
• Consequence: FLI1 ENST00000281428.12 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.53

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-CGAGAGAGA-C is Benign according to our data. Variant chr11-128693941-CGAGAGAGA-C is described in ClinVar as [Benign]. Clinvar id is 1232949.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SENCR	NR_038908.1	n.112-558_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.112-558_112-551del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0409 AC: 3385 AN: 82750 Hom.: 101 Cov.: 0

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.00177

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0246

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.00714

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0363

GnomAD4 exome AF: 0.0667 AC: 6116 AN: 91640 Hom.: 2 AF XY: 0.0639 AC XY: 2780 AN XY: 43534

Gnomad4 AFR exome AF: 0.110

Gnomad4 AMR exome AF: 0.0664

Gnomad4 ASJ exome AF: 0.0550

Gnomad4 EAS exome AF: 0.101

Gnomad4 SAS exome AF: 0.0428

Gnomad4 FIN exome AF: 0.0785

Gnomad4 NFE exome AF: 0.0591

Gnomad4 OTH exome AF: 0.0639

GnomAD4 genome AF: 0.0409 AC: 3385 AN: 82774 Hom.: 101 Cov.: 0 AF XY: 0.0428 AC XY: 1635 AN XY: 38162

Gnomad4 AFR AF: 0.0897

Gnomad4 AMR AF: 0.0323

Gnomad4 ASJ AF: 0.0246

Gnomad4 EAS AF: 0.0772

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.0611

Gnomad4 NFE AF: 0.0203

Gnomad4 OTH AF: 0.0368

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 19, 2021

- -

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;