ENST00000776366.1:n.130+1311T>C

Variant names:

• chr21-38964966-A-G
• rs2836788
• ENST00000776366.1:n.130+1311T>C

Variant summary

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

The ENST00000776366.1(ETS2-AS1):​n.130+1311T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 150,252 control chromosomes in the GnomAD database, including 38,925 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 0.72 (38925 hom., cov: 26)
• Consequence: ETS2-AS1 ENST00000776366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 1 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776366.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETS2-AS1	ENST00000776366.1		n.130+1311T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 107816 AN: 150142 Hom.: 38898 Cov.: 26

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.718 AC: 107888 AN: 150252 Hom.: 38925 Cov.: 26 AF XY: 0.716 AC XY: 52423 AN XY: 73174

African (AFR) AF: 0.796 AC: 32494 AN: 40834

American (AMR) AF: 0.633 AC: 9516 AN: 15034

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2285 AN: 3464

East Asian (EAS) AF: 0.617 AC: 3117 AN: 5050

South Asian (SAS) AF: 0.679 AC: 3231 AN: 4760

European-Finnish (FIN) AF: 0.725 AC: 7304 AN: 10074

Middle Eastern (MID) AF: 0.625 AC: 180 AN: 288

European-Non Finnish (NFE) AF: 0.706 AC: 47833 AN: 67780

Other (OTH) AF: 0.671 AC: 1384 AN: 2064

Alfa AF: 0.708 Hom.: 19859

Bravo AF: 0.710

Asia WGS AF: 0.645 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.3
DANN	Benign	0.85
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2836788; hg19: chr21-40336891;