rs2836770

Variant names:

• chr21-38942780-A-G
• rs2836770
• ENST00000415824.1:n.129+13559T>C

Variant summary

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

The ENST00000415824.1(ENSG00000205622):​n.129+13559T>C variant causes a intron 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: ENSG00000205622 ENST00000415824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

Genes affected

ENSG00000205622 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000205622	ENST00000415824.1	n.129+13559T>C		intron_variant	Intron 1 of 3	5
ENSG00000205622	ENST00000701127.1	n.54+2802T>C		intron_variant	Intron 1 of 4

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;