rs859267

Variant names:

• chr17-15922707-A-C
• rs859267
• ENST00000784729.1:n.258-17318A>C

Your query was ambiguous. Multiple possible variants found:

• chr17-15922707-A-C
• chr17-15922707-A-G

Variant summary

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

The ENST00000784729.1(ENSG00000290377):​n.258-17318A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0456 in 152,258 control chromosomes in the GnomAD database, including 381 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 0.046 (381 hom., cov: 32)
• Consequence: ENSG00000290377 ENST00000784729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 5 publications found

Genes affected

ENSG00000290377 (HGNC:):

ADORA2B (HGNC:264): (adenosine A2b receptor) This gene encodes an adenosine receptor that is a member of the G protein-coupled receptor superfamily. This integral membrane protein stimulates adenylate cyclase activity in the presence of adenosine. This protein also interacts with netrin-1, which is involved in axon elongation. The gene is located near the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA2B	XM_047435373.1	c.-377-17318A>C		intron_variant	Intron 4 of 5		XP_047291329.1
ADORA2B	XM_047435374.1	c.-377-17318A>C		intron_variant	Intron 2 of 3		XP_047291330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290377	ENST00000784729.1	n.258-17318A>C		intron_variant	Intron 2 of 2
ENSG00000290377	ENST00000784730.1	n.414-17318A>C		intron_variant	Intron 4 of 5
ENSG00000290377	ENST00000784731.1	n.447-17318A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6928 AN: 152140 Hom.: 376 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0156

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00650

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0456 AC: 6948 AN: 152258 Hom.: 381 Cov.: 32 AF XY: 0.0470 AC XY: 3501 AN XY: 74460

African (AFR) AF: 0.126 AC: 5232 AN: 41520

American (AMR) AF: 0.0546 AC: 835 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00952 AC: 33 AN: 3468

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5186

South Asian (SAS) AF: 0.0164 AC: 79 AN: 4828

European-Finnish (FIN) AF: 0.0156 AC: 166 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00650 AC: 442 AN: 68026

Other (OTH) AF: 0.0308 AC: 65 AN: 2110

Alfa AF: 0.0198 Hom.: 344

Bravo AF: 0.0499

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.41
DANN	Benign	0.77
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs859267; hg19: chr17-15826021;