11-128540941-C-T

Position:

• chr11-128540941-C-T

Variant summary

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

The NM_001143820.2(ETS1):​c.214+15350G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,988 control chromosomes in the GnomAD database, including 26,809 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 0.59 (26809 hom., cov: 31)
• Consequence: ETS1 NM_001143820.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878

Genes affected

ETS1 (HGNC:3488): (ETS proto-oncogene 1, transcription factor) This gene encodes a member of the ETS family of transcription factors, which are defined by the presence of a conserved ETS DNA-binding domain that recognizes the core consensus DNA sequence GGAA/T in target genes. These proteins function either as transcriptional activators or repressors of numerous genes, and are involved in stem cell development, cell senescence and death, and tumorigenesis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Jul 2011]

ETS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ETS1	NM_001143820.2	c.214+15350G>A		intron_variant		ENST00000392668.8	NP_001137292.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ETS1	ENST00000392668.8	c.214+15350G>A		intron_variant		1	NM_001143820.2	ENSP00000376436.3
ETS1	ENST00000525404.5	n.284-4158G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89335 AN: 151870 Hom.: 26777 Cov.: 31

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.588 AC: 89419 AN: 151988 Hom.: 26809 Cov.: 31 AF XY: 0.598 AC XY: 44414 AN XY: 74296

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.560

Alfa AF: 0.560 Hom.: 3360

Bravo AF: 0.589

Asia WGS AF: 0.746 AC: 2592 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.46
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3809006; hg19: chr11-128410836;