chr5-148826877-G-A

Position:

chr5-148826877-G-A

Variant summary

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

The NM_000024.6(ADRB2):c.46G>A(p.Gly16Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 1,613,480 control chromosomes in the GnomAD database, including 123,825 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.43 ( 14150 hom., cov: 35)

Exomes 𝑓: 0.38 ( 109675 hom. )

Consequence

ADRB2
NM_000024.6 missense

Scores

Clinical Significance

drug response reviewed by expert panel O:1

Conservation

PhyloP100: 1.81

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]

ADRB2 links:

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 (MetaRNN=1.3175607E-4).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADRB2	NM_000024.6 linkuse as main transcript	c.46G>A	p.Gly16Arg	missense_variant	1/1	ENST00000305988.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADRB2	ENST00000305988.6 linkuse as main transcript	c.46G>A	p.Gly16Arg	missense_variant	1/1		NM_000024.6	P1

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64762

AN:

152090

Hom.:

14124

Cov.:

show subpopulations

Gnomad AFR

AF:

0.494

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.435

Gnomad ASJ

AF:

0.430

Gnomad EAS

AF:

0.545

Gnomad SAS

AF:

0.442

Gnomad FIN

AF:

0.445

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.421

GnomAD3 exomes

AF:

0.421

AC:

105701

AN:

251152

Hom.:

22853

AF XY:

0.418

AC XY:

56692

AN XY:

135786

show subpopulations

Gnomad AFR exome

AF:

0.494

Gnomad AMR exome

AF:

0.432

Gnomad ASJ exome

AF:

0.437

Gnomad EAS exome

AF:

0.564

Gnomad SAS exome

AF:

0.452

Gnomad FIN exome

AF:

0.437

Gnomad NFE exome

AF:

0.372

Gnomad OTH exome

AF:

0.405

GnomAD4 exome

AF:

0.384

AC:

561623

AN:

1461272

Hom.:

109675

Cov.:

AF XY:

0.385

AC XY:

280174

AN XY:

726918

show subpopulations

Gnomad4 AFR exome

AF:

0.494

Gnomad4 AMR exome

AF:

0.431

Gnomad4 ASJ exome

AF:

0.442

Gnomad4 EAS exome

AF:

0.525

Gnomad4 SAS exome

AF:

0.449

Gnomad4 FIN exome

AF:

0.429

Gnomad4 NFE exome

AF:

0.365

Gnomad4 OTH exome

AF:

0.399

GnomAD4 genome

AF:

0.426

AC:

64831

AN:

152208

Hom.:

14150

Cov.:

AF XY:

0.431

AC XY:

32097

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.493

Gnomad4 AMR

AF:

0.435

Gnomad4 ASJ

AF:

0.430

Gnomad4 EAS

AF:

0.544

Gnomad4 SAS

AF:

0.444

Gnomad4 FIN

AF:

0.445

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.428

Alfa

AF:

0.388

Hom.:

28828

Bravo

AF:

0.427

TwinsUK

AF:

0.363

AC:

1345

ALSPAC

AF:

0.375

AC:

1446

ESP6500AA

AF:

0.487

AC:

2147

ESP6500EA

AF:

0.378

AC:

3249

ExAC

AF:

0.420

AC:

51023

Asia WGS

AF:

0.487

AC:

1689

AN:

3478

EpiCase

AF:

0.371

EpiControl

AF:

0.367

ClinVar

Significance: drug response

Submissions summary: Other:1

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

salmeterol response - Efficacy

Other:1

drug response, reviewed by expert panel

curation

PharmGKB

Mar 24, 2021

PharmGKB Level of Evidence 2A: Variants in Level 2A clinical annotations are found in PharmGKB’s Tier 1 Very Important Pharmacogenes (VIPs). These variants are in known pharmacogenes, implying causation of drug phenotype is more likely. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2A clinical annotations must be supported by at least two independent publications. Drug-variant association: Efficacy

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.080

Eigen

Benign

-0.63

Eigen_PC

Benign

-0.58

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.79

MetaRNN

Benign

0.00013

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.90

MutationTaster

Benign

1.0

PrimateAI

Benign

0.40

PROVEAN

Benign

-0.36

REVEL

Benign

0.079

Sift

Benign

0.35

Sift4G

Benign

0.50

Polyphen

0.043

Vest4

0.043

MutPred

0.33

Gain of catalytic residue at G16 (P = 0.0533);

MPC

0.74

ClinPred

0.0071

GERP RS

3.7

Varity_R

0.097

gMVP

0.62

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over