rs2836754

Variant names:

• chr21-38919816-T-C
• rs2836754
• ENST00000776402.1:n.551A>G

Variant summary

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

The ENST00000776402.1(ETS2-AS1):​n.551A>G 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 0.501 in 152,000 control chromosomes in the GnomAD database, including 20,341 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 0.50 (20341 hom., cov: 31)
• Consequence: ETS2-AS1 ENST00000776402.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 95 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETS2-AS1	NR_120405.1	n.676+3822A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ETS2-AS1	ENST00000776402.1	n.551A>G		non_coding_transcript_exon_variant	Exon 4 of 5
ETS2-AS1	ENST00000380931.6	n.676+3822A>G		intron_variant	Intron 2 of 3	2
ETS2-AS1	ENST00000415824.1	n.276+3822A>G		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76137 AN: 151882 Hom.: 20336 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.501 AC: 76142 AN: 152000 Hom.: 20341 Cov.: 31 AF XY: 0.489 AC XY: 36320 AN XY: 74294

African (AFR) AF: 0.364 AC: 15068 AN: 41444

American (AMR) AF: 0.454 AC: 6943 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2106 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1803 AN: 5170

South Asian (SAS) AF: 0.302 AC: 1455 AN: 4814

European-Finnish (FIN) AF: 0.445 AC: 4697 AN: 10558

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42179 AN: 67932

Other (OTH) AF: 0.527 AC: 1113 AN: 2112

Alfa AF: 0.584 Hom.: 128685

Bravo AF: 0.504

Asia WGS AF: 0.314 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.38
DANN	Benign	0.21
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2836754; hg19: chr21-40291740;