21-38931504-G-T

Variant names:

• chr21-38931504-G-T
• rs2222994
• ENST00000776876.1:n.62G>T

Variant summary

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

The ENST00000776876.1(ENSG00000301185):​n.62G>T 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 0.666 in 152,130 control chromosomes in the GnomAD database, including 35,147 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 0.67 (35147 hom., cov: 33)
• Consequence: ENSG00000301185 ENST00000776876.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 4 publications found

Genes affected

ENSG00000301185 (HGNC:):

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETS2-AS1	NR_120405.1	n.620+6306C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301185	ENST00000776876.1	n.62G>T		non_coding_transcript_exon_variant	Exon 2 of 2
ETS2-AS1	ENST00000380931.6	n.620+6306C>A		intron_variant	Intron 1 of 3	2
ETS2-AS1	ENST00000415824.1	n.130-7720C>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101196 AN: 152012 Hom.: 35134 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.666 AC: 101250 AN: 152130 Hom.: 35147 Cov.: 33 AF XY: 0.673 AC XY: 50062 AN XY: 74388

African (AFR) AF: 0.461 AC: 19091 AN: 41444

American (AMR) AF: 0.648 AC: 9913 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2331 AN: 3470

East Asian (EAS) AF: 0.739 AC: 3825 AN: 5178

South Asian (SAS) AF: 0.777 AC: 3748 AN: 4822

European-Finnish (FIN) AF: 0.839 AC: 8903 AN: 10614

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51319 AN: 67994

Other (OTH) AF: 0.647 AC: 1366 AN: 2110

Alfa AF: 0.724 Hom.: 31789

Bravo AF: 0.638

Asia WGS AF: 0.726 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.60
DANN	Benign	0.74
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs2222994; hg19: chr21-40303428;