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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;