rs2779193

Variant names:

• chr17-15943221-A-G
• rs2779193
• XM_011523659.4:c.26+2794A>G

Variant summary

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

The XM_011523659.4(ADORA2B):​c.26+2794A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,282 control chromosomes in the GnomAD database, including 62,182 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 0.89 (62182 hom., cov: 34)
• Consequence: ADORA2B XM_011523659.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719
• Publications: 3 publications found

Genes affected

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA2B	XM_011523659.4	c.26+2794A>G		intron_variant	Intron 2 of 2		XP_011521961.1
ADORA2B	XM_047435373.1	c.26+2794A>G		intron_variant	Intron 5 of 5		XP_047291329.1
ADORA2B	XM_047435374.1	c.26+2794A>G		intron_variant	Intron 3 of 3		XP_047291330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135745 AN: 152164 Hom.: 62146 Cov.: 34

Gnomad AFR AF: 0.661

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.892 AC: 135829 AN: 152282 Hom.: 62182 Cov.: 34 AF XY: 0.893 AC XY: 66504 AN XY: 74470

African (AFR) AF: 0.661 AC: 27434 AN: 41514

American (AMR) AF: 0.920 AC: 14078 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3423 AN: 3470

East Asian (EAS) AF: 0.975 AC: 5053 AN: 5182

South Asian (SAS) AF: 0.982 AC: 4743 AN: 4828

European-Finnish (FIN) AF: 0.984 AC: 10458 AN: 10624

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67512 AN: 68040

Other (OTH) AF: 0.918 AC: 1940 AN: 2114

Alfa AF: 0.961 Hom.: 29567

Bravo AF: 0.877

Asia WGS AF: 0.956 AC: 3325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.55
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs2779193; hg19: chr17-15846535;