GeneBe

rs11168070

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000798472.1(ENSG00000303969):​n.376+1067G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ENSG00000303969
ENST00000798472.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0210

Publications

28 publications found
Variant links:
Genes affected
ADRB2 (HGNC:286): (adrenoceptor beta 2) This gene encodes beta-2-adrenergic receptor which is a member of the G protein-coupled receptor superfamily. This receptor is directly associated with one of its ultimate effectors, the class C L-type calcium channel Ca(V)1.2. This receptor-channel complex also contains a G protein, an adenylyl cyclase, cAMP-dependent kinase, and the counterbalancing phosphatase, PP2A. The assembly of the signaling complex provides a mechanism that ensures specific and rapid signaling by this G protein-coupled receptor. This receptor is also a transcription regulator of the alpha-synuclein gene, and together, both genes are believed to be associated with risk of Parkinson's Disease. This gene is intronless. Different polymorphic forms, point mutations, and/or downregulation of this gene are associated with nocturnal asthma, obesity, type 2 diabetes and cardiovascular disease. [provided by RefSeq, Oct 2019]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ADRB2NM_000024.6 linkc.-468G>A upstream_gene_variant ENST00000305988.6 NP_000015.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000303969ENST00000798472.1 linkn.376+1067G>A intron_variant Intron 3 of 4
ENSG00000303969ENST00000798473.1 linkn.349+1067G>A intron_variant Intron 3 of 4
ADRB2ENST00000305988.6 linkc.-468G>A upstream_gene_variant 6 NM_000024.6 ENSP00000305372.4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
39064
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
20182
African (AFR)
AF:
0.00
AC:
0
AN:
532
American (AMR)
AF:
0.00
AC:
0
AN:
3006
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
776
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1416
South Asian (SAS)
AF:
0.00
AC:
0
AN:
5654
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
1914
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
122
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
23626
Other (OTH)
AF:
0.00
AC:
0
AN:
2018
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
8.9
DANN
Benign
0.94
PhyloP100
0.021
PromoterAI
0.019
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs11168070; hg19: chr5-148205927; API