11-128693881-TG-T

Variant summary

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

The NR_038908.1(SENCR):n.112-491del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.77 (33169 hom., cov: 0)
  • Exomes 𝑓: 0.74 (24563 hom.)
• Consequence: SENCR NR_038908.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0940

Genes affected

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

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 -10 ACMG points.

• BP6: Variant 11-128693881-TG-T is Benign according to our data. Variant chr11-128693881-TG-T is described in ClinVar as [Benign]. Clinvar id is 1241437.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SENCR	NR_038908.1	n.112-491del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SENCR	ENST00000526269.2	n.112-491del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.774 AC: 92642 AN: 119640 Hom.: 33137 Cov.: 0

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.783

GnomAD4 exome AF: 0.743 AC: 68504 AN: 92218 Hom.: 24563 Cov.: 0 AF XY: 0.740 AC XY: 32379 AN XY: 43754

Gnomad4 AFR exome AF: 0.766

Gnomad4 AMR exome AF: 0.720

Gnomad4 ASJ exome AF: 0.824

Gnomad4 EAS exome AF: 0.718

Gnomad4 SAS exome AF: 0.710

Gnomad4 FIN exome AF: 0.591

Gnomad4 NFE exome AF: 0.742

Gnomad4 OTH exome AF: 0.768

GnomAD4 genome AF: 0.774 AC: 92719 AN: 119732 Hom.: 33169 Cov.: 0 AF XY: 0.775 AC XY: 44005 AN XY: 56794

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.781

Asia WGS AF: 0.660 AC: 2085 AN: 3160

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

- -

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: rs55635129; hg19: chr11-128563776;