rs2836716

chr21-38864135-G-A

Variant summary

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

The ENST00000663561.1(ETS2-AS1):n.534+37766C>T variant causes a intron, non coding transcript 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 ENST00000663561.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETS2-AS1	ENST00000663561.1	n.534+37766C>T		intron_variant, non_coding_transcript_variant
ETS2-AS1	ENST00000626259.2	n.314C>T		non_coding_transcript_exon_variant	4/4	5
ETS2-AS1	ENST00000689146.2	n.658C>T		non_coding_transcript_exon_variant	3/3
ETS2-AS1	ENST00000701265.1	n.911C>T		non_coding_transcript_exon_variant	4/4

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0538

Gnomad4 NFE exome AF: 0.0395

Gnomad4 OTH exome AF: 0.0833

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

Gnomad4 AFR AF: 0.0311

Gnomad4 AMR AF: 0.0397

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0146

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.0947

Gnomad4 OTH AF: 0.0451

Alfa AF: 0.0794 Hom.: 697

Bravo AF: 0.0576

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.4
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836716; hg19: chr21-40236059;