rs2836753

Positions:

• chr21-38919263-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+4375A>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 152,110 control chromosomes in the GnomAD database, including 20,377 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 (20375 hom., cov: 33)
  • Exomes 𝑓: 0.75 (2 hom.)
• Consequence: ETS2-AS1 NR_120405.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

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=-0.9).
• 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+4375A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ETS2-AS1	ENST00000615324.2	n.382A>G		non_coding_transcript_exon_variant	3/3
ETS2-AS1	ENST00000660602.1	n.782A>G		non_coding_transcript_exon_variant	3/3
ETS2-AS1	ENST00000380931.6	n.676+4375A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76219 AN: 151984 Hom.: 20370 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 2 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.501 AC: 76224 AN: 152102 Hom.: 20375 Cov.: 33 AF XY: 0.489 AC XY: 36366 AN XY: 74352

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.528

Alfa AF: 0.518 Hom.: 4037

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	-0.90
CADD	Benign	8.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836753; hg19: chr21-40291187;