chr5-148827083-G-A

Variant names:

• chr5-148827083-G-A
• rs1042717
• NM_000024.6:c.252G>A

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_000024.6(ADRB2):​c.252G>A​(p.Leu84Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 1,613,882 control chromosomes in the GnomAD database, including 40,788 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.25 (5206 hom., cov: 33)
  • Exomes 𝑓: 0.21 (35582 hom.)
• Consequence: ADRB2 NM_000024.6 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0760
• Publications: 63 publications found

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]

ENSG00000303969 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP6: Variant 5-148827083-G-A is Benign according to our data. Variant chr5-148827083-G-A is described in ClinVar as Benign. ClinVar VariationId is 1225464.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.076 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000024.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADRB2	NM_000024.6	MANE Select	c.252G>A	p.Leu84Leu	synonymous	Exon 1 of 1	NP_000015.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADRB2	ENST00000305988.6	TSL:6 MANE Select	c.252G>A	p.Leu84Leu	synonymous	Exon 1 of 1	ENSP00000305372.4
	ENSG00000303969	ENST00000798472.1		n.376+1786G>A		intron	N/A
	ENSG00000303969	ENST00000798473.1		n.349+1786G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38092 AN: 152092 Hom.: 5203 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.264

GnomAD2 exomes AF: 0.257 AC: 64399 AN: 250862 AF XY: 0.255

Gnomad AFR exome AF: 0.326

Gnomad AMR exome AF: 0.392

Gnomad ASJ exome AF: 0.208

Gnomad EAS exome AF: 0.331

Gnomad FIN exome AF: 0.156

Gnomad NFE exome AF: 0.196

Gnomad OTH exome AF: 0.246

GnomAD4 exome AF: 0.211 AC: 308624 AN: 1461670 Hom.: 35582 Cov.: 57 AF XY: 0.215 AC XY: 156149 AN XY: 727124

African (AFR) AF: 0.334 AC: 11166 AN: 33478

American (AMR) AF: 0.386 AC: 17216 AN: 44652

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 5359 AN: 26136

East Asian (EAS) AF: 0.366 AC: 14530 AN: 39690

South Asian (SAS) AF: 0.337 AC: 29056 AN: 86248

European-Finnish (FIN) AF: 0.161 AC: 8589 AN: 53410

Middle Eastern (MID) AF: 0.321 AC: 1851 AN: 5766

European-Non Finnish (NFE) AF: 0.186 AC: 207230 AN: 1111898

Other (OTH) AF: 0.226 AC: 13627 AN: 60392

GnomAD4 genome AF: 0.250 AC: 38116 AN: 152212 Hom.: 5206 Cov.: 33 AF XY: 0.251 AC XY: 18689 AN XY: 74428

African (AFR) AF: 0.324 AC: 13463 AN: 41508

American (AMR) AF: 0.322 AC: 4918 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1782 AN: 5170

South Asian (SAS) AF: 0.350 AC: 1686 AN: 4822

European-Finnish (FIN) AF: 0.159 AC: 1690 AN: 10610

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12965 AN: 68016

Other (OTH) AF: 0.263 AC: 555 AN: 2112

Alfa AF: 0.216 Hom.: 17761

Bravo AF: 0.264

Asia WGS AF: 0.345 AC: 1198 AN: 3478

EpiCase AF: 0.209

EpiControl AF: 0.218

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	6.7
DANN	Benign	0.89
PhyloP100		0.076
PromoterAI		-0.042	Neutral
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1042717; hg19: chr5-148206646; COSMIC: COSV60005777;