rs758857

Variant summary

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

The NM_000676.4(ADORA2B):​c.335+5360G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,224 control chromosomes in the GnomAD database, including 38,039 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 0.67 ( 38039 hom., cov: 35)

Consequence

ADORA2B
NM_000676.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.66
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=-1.0).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ADORA2BNM_000676.4 linkuse as main transcriptc.335+5360G>A intron_variant ENST00000304222.3 NP_000667.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADORA2BENST00000304222.3 linkuse as main transcriptc.335+5360G>A intron_variant 1 NM_000676.4 ENSP00000304501 P1

Frequencies

GnomAD3 genomes
AF:
0.673
AC:
102406
AN:
152106
Hom.:
38035
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.338
Gnomad AMI
AF:
0.784
Gnomad AMR
AF:
0.693
Gnomad ASJ
AF:
0.874
Gnomad EAS
AF:
0.665
Gnomad SAS
AF:
0.721
Gnomad FIN
AF:
0.846
Gnomad MID
AF:
0.791
Gnomad NFE
AF:
0.829
Gnomad OTH
AF:
0.740
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.673
AC:
102427
AN:
152224
Hom.:
38039
Cov.:
35
AF XY:
0.675
AC XY:
50260
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.338
Gnomad4 AMR
AF:
0.693
Gnomad4 ASJ
AF:
0.874
Gnomad4 EAS
AF:
0.666
Gnomad4 SAS
AF:
0.721
Gnomad4 FIN
AF:
0.846
Gnomad4 NFE
AF:
0.829
Gnomad4 OTH
AF:
0.740
Alfa
AF:
0.797
Hom.:
69341
Bravo
AF:
0.648
Asia WGS
AF:
0.678
AC:
2357
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.045
DANN
Benign
0.64

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: rs758857; hg19: chr17-15854257; API