rs1042717
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_000024.6(ADRB2):c.252G>A(p.Leu84=) 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
NM_000024.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0760
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 made for transcript
Verdict is Benign. Variant got -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 id 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.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADRB2 | NM_000024.6 | c.252G>A | p.Leu84= | synonymous_variant | 1/1 | ENST00000305988.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADRB2 | ENST00000305988.6 | c.252G>A | p.Leu84= | synonymous_variant | 1/1 | NM_000024.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.250 AC: 38092AN: 152092Hom.: 5203 Cov.: 33
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GnomAD3 exomes AF: 0.257 AC: 64399AN: 250862Hom.: 9191 AF XY: 0.255 AC XY: 34598AN XY: 135596
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GnomAD4 exome AF: 0.211 AC: 308624AN: 1461670Hom.: 35582 Cov.: 57 AF XY: 0.215 AC XY: 156149AN XY: 727124
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GnomAD4 genome ? AF: 0.250 AC: 38116AN: 152212Hom.: 5206 Cov.: 33 AF XY: 0.251 AC XY: 18689AN XY: 74428
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at