rs2779212

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000676.4(ADORA2B):​c.336-1338T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,132 control chromosomes in the GnomAD database, including 27,941 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 0.60 ( 27941 hom., cov: 32)

Consequence

ADORA2B
NM_000676.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.326
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADORA2BNM_000676.4 linkuse as main transcriptc.336-1338T>C intron_variant ENST00000304222.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADORA2BENST00000304222.3 linkuse as main transcriptc.336-1338T>C intron_variant 1 NM_000676.4 P1

Frequencies

GnomAD3 genomes
AF:
0.599
AC:
91123
AN:
152014
Hom.:
27890
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.697
Gnomad AMI
AF:
0.538
Gnomad AMR
AF:
0.542
Gnomad ASJ
AF:
0.682
Gnomad EAS
AF:
0.270
Gnomad SAS
AF:
0.538
Gnomad FIN
AF:
0.606
Gnomad MID
AF:
0.642
Gnomad NFE
AF:
0.579
Gnomad OTH
AF:
0.588
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.600
AC:
91242
AN:
152132
Hom.:
27941
Cov.:
32
AF XY:
0.598
AC XY:
44455
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.697
Gnomad4 AMR
AF:
0.542
Gnomad4 ASJ
AF:
0.682
Gnomad4 EAS
AF:
0.270
Gnomad4 SAS
AF:
0.539
Gnomad4 FIN
AF:
0.606
Gnomad4 NFE
AF:
0.579
Gnomad4 OTH
AF:
0.591
Alfa
AF:
0.497
Hom.:
2232
Bravo
AF:
0.597
Asia WGS
AF:
0.467
AC:
1621
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.1
DANN
Benign
0.45

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2779212; hg19: chr17-15876655; COSMIC: COSV58483412; COSMIC: COSV58483412; API