rs2836770

chr21-38942780-A-G

Variant summary

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

The ENST00000415824.1(ETS2-AS1):n.129+13559T>C 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 0.56 in 152,018 control chromosomes in the GnomAD database, including 24,358 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 0.56 (24358 hom., cov: 32)
• Consequence: ETS2-AS1 ENST00000415824.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 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	ENST00000415824.1	n.129+13559T>C		intron_variant, non_coding_transcript_variant		5
ETS2-AS1	ENST00000701127.1	n.54+2802T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84988 AN: 151900 Hom.: 24323 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.560 AC: 85083 AN: 152018 Hom.: 24358 Cov.: 32 AF XY: 0.567 AC XY: 42124 AN XY: 74296

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.537

Alfa AF: 0.509 Hom.: 40680

Bravo AF: 0.549

Asia WGS AF: 0.719 AC: 2498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.6
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836770; hg19: chr21-40314704;