rs2142109

chr21-38930032-C-Tchr21-38930032-C-G

Variant summary

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

The NR_120405.1(ETS2-AS1):n.621-6339G>A 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 0.785 in 152,240 control chromosomes in the GnomAD database, including 47,912 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 0.79 (47912 hom., cov: 34)
• Consequence: ETS2-AS1 NR_120405.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETS2-AS1	NR_120405.1	n.621-6339G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETS2-AS1	ENST00000380931.6	n.621-6339G>A		intron_variant, non_coding_transcript_variant		2
ETS2-AS1	ENST00000415824.1	n.130-6248G>A		intron_variant, non_coding_transcript_variant		5
ETS2-AS1	ENST00000701127.1	n.55-6339G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119468 AN: 152122 Hom.: 47898 Cov.: 34

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.785 AC: 119535 AN: 152240 Hom.: 47912 Cov.: 34 AF XY: 0.790 AC XY: 58780 AN XY: 74440

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.764

Alfa AF: 0.828 Hom.: 37504

Bravo AF: 0.764

Asia WGS AF: 0.830 AC: 2888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.0
Dann	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2142109; hg19: chr21-40301956;