rs717871

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000380931.6(ENSG00000205622):​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: ENSG00000205622 ENST00000380931.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

Genes affected

ENSG00000205622 (HGNC:56712): (ETS2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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
ENSG00000205622	ENST00000380931.6	n.742-5159A>G		intron_variant	Intron 3 of 3	2
ENSG00000205622	ENST00000415824.1	n.342-5159A>G		intron_variant	Intron 3 of 3	5
ENSG00000205622	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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0520

Gnomad4 ASJ AF: 0.0409

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0715

Gnomad4 NFE AF: 0.0953

Gnomad4 OTH AF: 0.0686

Alfa AF: 0.0903 Hom.: 304

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs717871; hg19: chr21-40257455;