rs2836716

Variant names:

• chr21-38864135-G-A
• rs2836716
• ENST00000626259.2:n.314C>T

Variant summary

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

The ENST00000626259.2(ENSG00000205622):​n.314C>T 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 0.0628 in 152,590 control chromosomes in the GnomAD database, including 405 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 0.063 (405 hom., cov: 31)
  • Exomes 𝑓: 0.046 (0 hom.)
• Consequence: ENSG00000205622 ENST00000626259.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

ENSG00000205622 (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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000205622	ENST00000626259.2	n.314C>T		non_coding_transcript_exon_variant	Exon 4 of 4	5
ENSG00000205622	ENST00000689146.2	n.658C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000205622	ENST00000701265.1	n.911C>T		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000205622	ENST00000663561.1	n.534+37766C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0628 AC: 9549 AN: 152020 Hom.: 402 Cov.: 31

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.0455

GnomAD4 exome AF: 0.0465 AC: 21 AN: 452 Hom.: 0 Cov.: 0 AF XY: 0.0399 AC XY: 11 AN XY: 276

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0538

Gnomad4 NFE exome AF: 0.0395

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.0628 AC: 9561 AN: 152138 Hom.: 405 Cov.: 31 AF XY: 0.0602 AC XY: 4474 AN XY: 74356

Gnomad4 AFR AF: 0.0311

Gnomad4 AMR AF: 0.0397

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0146

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.0947

Gnomad4 OTH AF: 0.0451

Alfa AF: 0.0794 Hom.: 697

Bravo AF: 0.0576

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836716; hg19: chr21-40236059;