rs1128334

chr11-128459064-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001143820.2(ETS1):c.*3297G>A variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.111 in 150,688 control chromosomes in the GnomAD database, including 1,135 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 0.11 (1134 hom., cov: 31)
  • Exomes 𝑓: 0.090 (1 hom.)
• Consequence: ETS1 NM_001143820.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.92

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETS1	NM_001143820.2	c.*3297G>A		3_prime_UTR_variant	10/10	ENST00000392668.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETS1	ENST00000392668.8	c.*3297G>A		3_prime_UTR_variant	10/10	1	NM_001143820.2
ETS1	ENST00000319397.7	c.*3297G>A		3_prime_UTR_variant	8/8	1		P1
ETS1	ENST00000535549.5	c.*3297G>A		3_prime_UTR_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16690 AN: 150128 Hom.: 1131 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0900

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.0385

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0940

GnomAD4 exome AF: 0.0897 AC: 40 AN: 446 Hom.: 1 Cov.: 0 AF XY: 0.0896 AC XY: 24 AN XY: 268

Gnomad4 EAS exome AF: 0.0455

Gnomad4 FIN exome AF: 0.0933

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.111 AC: 16715 AN: 150242 Hom.: 1134 Cov.: 31 AF XY: 0.113 AC XY: 8278 AN XY: 73290

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0901

Gnomad4 ASJ AF: 0.0639

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0943

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0944

Alfa AF: 0.107 Hom.: 1966

Bravo AF: 0.106

Asia WGS AF: 0.208 AC: 713 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
Cadd	Benign	18
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1128334; hg19: chr11-128328959;