Genetic Variant SENCR:n.112-491delC (chr11-128693881-TG-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000526269.2(SENCR):n.112-491delC variant causes a intron 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
ENST00000526269.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0940

Publications

1 publications found

Variant links:

Genes affected

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

SENCR links:

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]

FLI1 Gene-Disease associations (from GenCC):

bleeding disorder, platelet-type, 21
Inheritance: AD, AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen

FLI1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FLI1	NM_002017.5 link	c.-377delG		upstream_gene_variant		ENST00000527786.7	NP_002008.2	Q01543-1A0A024R3M5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLI1	ENST00000527786.7 link	c.-377delG		upstream_gene_variant		1	NM_002017.5	ENSP00000433488.2		Q01543-1

Frequencies

GnomAD3 genomes

AF:

0.774

AC:

92642

AN:

119640

Hom.:

33137

Cov.:

show subpopulations

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.:

AF XY:

0.740

AC XY:

32379

AN XY:

43754

show subpopulations

African (AFR)

AF:

0.766

AC:

3147

AN:

4110

American (AMR)

AF:

0.720

AC:

1968

AN:

2734

Ashkenazi Jewish (ASJ)

AF:

0.824

AC:

4478

AN:

5432

East Asian (EAS)

AF:

0.718

AC:

7862

AN:

10946

South Asian (SAS)

AF:

0.710

AC:

1344

AN:

1892

European-Finnish (FIN)

AF:

0.591

AC:

1264

AN:

2138

Middle Eastern (MID)

AF:

0.806

AC:

464

AN:

576

European-Non Finnish (NFE)

AF:

0.742

AC:

42335

AN:

57040

Other (OTH)

AF:

0.768

AC:

5642

AN:

7350

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

1093

2186

3278

4371

5464

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.774

AC:

92719

AN:

119732

Hom.:

33169

Cov.:

AF XY:

0.775

AC XY:

44005

AN XY:

56794

show subpopulations

African (AFR)

AF:

0.794

AC:

24616

AN:

30994

American (AMR)

AF:

0.764

AC:

9016

AN:

11794

Ashkenazi Jewish (ASJ)

AF:

0.819

AC:

2613

AN:

3190

East Asian (EAS)

AF:

0.767

AC:

3053

AN:

3982

South Asian (SAS)

AF:

0.783

AC:

2799

AN:

3576

European-Finnish (FIN)

AF:

0.743

AC:

4276

AN:

5754

Middle Eastern (MID)

AF:

0.851

AC:

223

AN:

262

European-Non Finnish (NFE)

AF:

0.766

AC:

44206

AN:

57740

Other (OTH)

AF:

0.781

AC:

1290

AN:

1652

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.535

Heterozygous variant carriers

1205

2410

3614

4819

6024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Asia WGS

AF:

0.660

AC:

2085

AN:

3160

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 18, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.094

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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11-128693881-TG-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over