21-38919263-T-C

Variant names:

• chr21-38919263-T-C
• rs2836753
• ENST00000615324.3:n.540A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000615324.3(ETS2-AS1):​n.540A>G variant causes a non coding transcript exon 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 ENST00000615324.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 10 publications found

Genes affected

ETS2-AS1 (HGNC:56712): (ETS2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ETS2-AS1	NR_120405.1	n.676+4375A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ETS2-AS1	ENST00000615324.3	n.540A>G		non_coding_transcript_exon_variant	Exon 4 of 4	6
ETS2-AS1	ENST00000660602.1	n.782A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ETS2-AS1	ENST00000776399.1	n.755A>G		non_coding_transcript_exon_variant	Exon 4 of 4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.364 AC: 15094 AN: 41488

American (AMR) AF: 0.454 AC: 6937 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2108 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1802 AN: 5168

South Asian (SAS) AF: 0.303 AC: 1460 AN: 4826

European-Finnish (FIN) AF: 0.446 AC: 4713 AN: 10568

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42218 AN: 67986

Other (OTH) AF: 0.528 AC: 1111 AN: 2106

Alfa AF: 0.515 Hom.: 4102

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2836753; hg19: chr21-40291187;