rs7117932

chr11-128567058-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.69+6004G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,056 control chromosomes in the GnomAD database, including 11,129 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 0.37 (11129 hom., cov: 32)
• Consequence: ETS1 NM_001143820.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

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]

LOC105369565 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETS1	NM_001143820.2	c.69+6004G>A		intron_variant		ENST00000392668.8
LOC105369565	XR_948163.3	n.717+602C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETS1	ENST00000392668.8	c.69+6004G>A		intron_variant		1	NM_001143820.2
ETS1	ENST00000525404.5	n.138+6004G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56223 AN: 151938 Hom.: 11141 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.370 AC: 56208 AN: 152056 Hom.: 11129 Cov.: 32 AF XY: 0.368 AC XY: 27372 AN XY: 74316

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.360

Alfa AF: 0.427 Hom.: 23234

Bravo AF: 0.353

Asia WGS AF: 0.275 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.7
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7117932; hg19: chr11-128436953;