rs717871

chr21-38885531-T-C

Variant summary

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

The NR_120405.1(ETS2-AS1):n.742-5159A>G variant causes a intron, non coding transcript 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 NR_120405.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379

Genes affected

ETS2-AS1 (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/exons	MANE	UniProt
ETS2-AS1	NR_120405.1	n.742-5159A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETS2-AS1	ENST00000663561.1	n.534+16370A>G		intron_variant, non_coding_transcript_variant

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;