21-38930032-C-T

Variant names:

• chr21-38930032-C-T
• rs2142109
• ENST00000380931.6:n.621-6339G>A

Variant summary

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

The ENST00000380931.6(ETS2-AS1):​n.621-6339G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,240 control chromosomes in the GnomAD database, including 47,912 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 0.79 (47912 hom., cov: 34)
• Consequence: ETS2-AS1 ENST00000380931.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 1 publications found

Genes affected

ETS2-AS1 (HGNC:56712): (ETS2 antisense RNA 1)

ENSG00000301185 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000380931.6. 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
	ETS2-AS1	NR_120405.1		n.621-6339G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETS2-AS1	ENST00000380931.6	TSL:2	n.621-6339G>A		intron	N/A
	ETS2-AS1	ENST00000415824.1	TSL:5	n.130-6248G>A		intron	N/A
	ETS2-AS1	ENST00000615324.3	TSL:6	n.143-6339G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119468 AN: 152122 Hom.: 47898 Cov.: 34

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.785 AC: 119535 AN: 152240 Hom.: 47912 Cov.: 34 AF XY: 0.790 AC XY: 58780 AN XY: 74440

African (AFR) AF: 0.627 AC: 26028 AN: 41524

American (AMR) AF: 0.749 AC: 11452 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3470

East Asian (EAS) AF: 0.830 AC: 4300 AN: 5182

South Asian (SAS) AF: 0.881 AC: 4250 AN: 4826

European-Finnish (FIN) AF: 0.899 AC: 9542 AN: 10616

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58727 AN: 68018

Other (OTH) AF: 0.764 AC: 1616 AN: 2116

Alfa AF: 0.826 Hom.: 44243

Bravo AF: 0.764

Asia WGS AF: 0.830 AC: 2888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.10
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2142109; hg19: chr21-40301956;