rs717871

Variant names:

• chr21-38885531-T-C
• rs717871
• ENST00000380931.6:n.742-5159A>G

Variant summary

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

The ENST00000380931.6(ETS2-AS1):​n.742-5159A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,208 control chromosomes in the GnomAD database, including 731 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 0.093 (731 hom., cov: 33)
• Consequence: ETS2-AS1 ENST00000380931.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETS2-AS1	NR_120405.1	n.742-5159A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ETS2-AS1	ENST00000380931.6	n.742-5159A>G		intron_variant	Intron 3 of 3	2
ETS2-AS1	ENST00000415824.1	n.342-5159A>G		intron_variant	Intron 3 of 3	5
ETS2-AS1	ENST00000626259.2	n.223+16370A>G		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14049 AN: 152090 Hom.: 725 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0715

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0953

Gnomad OTH AF: 0.0693

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

GnomAD4 genome AF: 0.0925 AC: 14084 AN: 152208 Hom.: 731 Cov.: 33 AF XY: 0.0890 AC XY: 6622 AN XY: 74414

African (AFR) AF: 0.132 AC: 5469 AN: 41494

American (AMR) AF: 0.0520 AC: 796 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0409 AC: 142 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5180

South Asian (SAS) AF: 0.0257 AC: 124 AN: 4826

European-Finnish (FIN) AF: 0.0715 AC: 758 AN: 10596

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0953 AC: 6483 AN: 68024

Other (OTH) AF: 0.0686 AC: 145 AN: 2114

Alfa AF: 0.0908 Hom.: 341

Bravo AF: 0.0914

Asia WGS AF: 0.0250 AC: 87 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	1.8
DANN	Benign	0.56
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs717871; hg19: chr21-40257455;