rs2836754

chr21-38919816-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.676+3822A>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 0.501 in 152,000 control chromosomes in the GnomAD database, including 20,341 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 0.50 (20341 hom., cov: 31)
• Consequence: ETS2-AS1 NR_120405.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ETS2-AS1	NR_120405.1	n.676+3822A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETS2-AS1	ENST00000380931.6	n.676+3822A>G		intron_variant, non_coding_transcript_variant		2
ETS2-AS1	ENST00000415824.1	n.276+3822A>G		intron_variant, non_coding_transcript_variant		5
ETS2-AS1	ENST00000613045.1	n.521+3610A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76137 AN: 151882 Hom.: 20336 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.501 AC: 76142 AN: 152000 Hom.: 20341 Cov.: 31 AF XY: 0.489 AC XY: 36320 AN XY: 74294

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.527

Alfa AF: 0.594 Hom.: 64066

Bravo AF: 0.504

Asia WGS AF: 0.314 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.38
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836754; hg19: chr21-40291740;