chr21-38942780-A-G

Variant names:

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

Variant summary

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

The ENST00000701127.1(ETS2-AS1):​n.54+2802T>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: ETS2-AS1 ENST00000701127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 8 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701127.1. 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	ENST00000415824.1	TSL:5	n.129+13559T>C		intron	N/A
	ETS2-AS1	ENST00000615324.3	TSL:6	n.142+2802T>C		intron	N/A
	ETS2-AS1	ENST00000701127.1		n.54+2802T>C		intron	N/A

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

African (AFR) AF: 0.659 AC: 27304 AN: 41462

American (AMR) AF: 0.491 AC: 7508 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1755 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3677 AN: 5160

South Asian (SAS) AF: 0.764 AC: 3685 AN: 4822

European-Finnish (FIN) AF: 0.567 AC: 5986 AN: 10562

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33514 AN: 67946

Other (OTH) AF: 0.537 AC: 1133 AN: 2110

Alfa AF: 0.513 Hom.: 87403

Bravo AF: 0.549

Asia WGS AF: 0.719 AC: 2498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2836770; hg19: chr21-40314704;