rs2070531

Positions:

• chr21-38822292-C-T

Variant summary

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

The NM_005239.6(ETS2):​c.1195-382C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,092 control chromosomes in the GnomAD database, including 9,135 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 0.34 (9135 hom., cov: 32)
• Consequence: ETS2 NM_005239.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

Genes affected

ETS2 (HGNC:3489): (ETS proto-oncogene 2, transcription factor) This gene encodes a transcription factor which regulates genes involved in development and apoptosis. The encoded protein is also a protooncogene and shown to be involved in regulation of telomerase. A pseudogene of this gene is located on the X chromosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]

ETS2-AS1 (HGNC:56712): (ETS2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ETS2	NM_005239.6	c.1195-382C>T		intron_variant		ENST00000360938.8	NP_005230.1
ETS2	NM_001256295.2	c.1615-382C>T		intron_variant			NP_001243224.1
ETS2	XM_005260935.2	c.1195-382C>T		intron_variant			XP_005260992.1
ETS2	XM_017028290.2	c.1195-382C>T		intron_variant			XP_016883779.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ETS2	ENST00000360938.8	c.1195-382C>T		intron_variant		1	NM_005239.6	ENSP00000354194	P1
ETS2-AS1	ENST00000663561.1	n.535-8867G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52289 AN: 151974 Hom.: 9131 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.344 AC: 52317 AN: 152092 Hom.: 9135 Cov.: 32 AF XY: 0.343 AC XY: 25475 AN XY: 74358

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.323

Alfa AF: 0.349 Hom.: 12651

Bravo AF: 0.338

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.3
DANN	Benign	0.40

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

LitVar

Other links and lift over

dbSNP: rs2070531; hg19: chr21-40194216;