rs2836716

Variant names:

• chr21-38864135-G-A
• rs2836716
• ENST00000626259.2:n.314C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000689146.3(ETS2-AS1):​n.660C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0628 in 152,590 control chromosomes in the GnomAD database, including 405 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 0.063 (405 hom., cov: 31)
  • Exomes 𝑓: 0.046 (0 hom.)
• Consequence: ETS2-AS1 ENST00000689146.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000689146.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETS2-AS1	ENST00000626259.2	TSL:5	n.314C>T		non_coding_transcript_exon	Exon 4 of 4
	ETS2-AS1	ENST00000689146.3		n.660C>T		non_coding_transcript_exon	Exon 3 of 3
	ETS2-AS1	ENST00000701265.1		n.911C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0628 AC: 9549 AN: 152020 Hom.: 402 Cov.: 31

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.0455

GnomAD4 exome AF: 0.0465 AC: 21 AN: 452 Hom.: 0 Cov.: 0 AF XY: 0.0399 AC XY: 11 AN XY: 276

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.00 AC: 0 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 8

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.0538 AC: 14 AN: 260

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0395 AC: 6 AN: 152

Other (OTH) AF: 0.0833 AC: 1 AN: 12

GnomAD4 genome AF: 0.0628 AC: 9561 AN: 152138 Hom.: 405 Cov.: 31 AF XY: 0.0602 AC XY: 4474 AN XY: 74356

African (AFR) AF: 0.0311 AC: 1292 AN: 41502

American (AMR) AF: 0.0397 AC: 606 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3472

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5170

South Asian (SAS) AF: 0.0146 AC: 70 AN: 4810

European-Finnish (FIN) AF: 0.0717 AC: 760 AN: 10596

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0947 AC: 6441 AN: 67996

Other (OTH) AF: 0.0451 AC: 95 AN: 2108

Alfa AF: 0.0775 Hom.: 867

Bravo AF: 0.0576

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2836716; hg19: chr21-40236059;