rs2410062

Variant names:

• chr21-38856996-A-G
• rs2410062
• ENST00000776368.1:n.880T>C

Variant summary

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

The ENST00000776368.1(ETS2-AS1):​n.880T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,192 control chromosomes in the GnomAD database, including 3,003 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 0.17 (3003 hom., cov: 32)
• Consequence: ETS2-AS1 ENST00000776368.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 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
ETS2-AS1	ENST00000776368.1	n.880T>C		non_coding_transcript_exon_variant	Exon 4 of 4
ETS2-AS1	ENST00000663561.1	n.535-43571T>C		intron_variant	Intron 2 of 2
ETS2-AS1	ENST00000686487.3	n.1587-35158T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25257 AN: 152074 Hom.: 3002 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.166 AC: 25286 AN: 152192 Hom.: 3003 Cov.: 32 AF XY: 0.159 AC XY: 11818 AN XY: 74436

African (AFR) AF: 0.331 AC: 13755 AN: 41504

American (AMR) AF: 0.105 AC: 1606 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3468

East Asian (EAS) AF: 0.0433 AC: 224 AN: 5178

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4826

European-Finnish (FIN) AF: 0.0446 AC: 474 AN: 10618

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7869 AN: 67992

Other (OTH) AF: 0.174 AC: 367 AN: 2114

Alfa AF: 0.151 Hom.: 442

Bravo AF: 0.182

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.49
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2410062; hg19: chr21-40228920;