rs7930515

Positions:

• chr11-128694899-A-C
• chr11-128694899-A-T

Variant summary

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

The NM_002017.5(FLI1):​c.18+623A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,032 control chromosomes in the GnomAD database, including 38,492 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 0.71 (38492 hom., cov: 34)
• Consequence: FLI1 NM_002017.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FLI1	NM_002017.5	c.18+623A>C		intron_variant		ENST00000527786.7
SENCR	NR_038908.1	n.111+1014T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLI1	ENST00000527786.7	c.18+623A>C		intron_variant		1	NM_002017.5	P1
SENCR	ENST00000526269.2	n.111+1014T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107989 AN: 151922 Hom.: 38455 Cov.: 34

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.711 AC: 108080 AN: 152032 Hom.: 38492 Cov.: 34 AF XY: 0.709 AC XY: 52676 AN XY: 74324

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.719

Alfa AF: 0.705 Hom.: 42874

Bravo AF: 0.716

Asia WGS AF: 0.677 AC: 2351 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7930515; hg19: chr11-128564794;