Variant rs2228079 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000674.3(ADORA1):c.306T>G(p.Ala102=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,613,614 control chromosomes in the GnomAD database, including 84,762 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 0.26 ( 6012 hom., cov: 32)

Exomes 𝑓: 0.32 ( 78750 hom. )

Consequence

ADORA1
NM_000674.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.95

Variant links:

Genes affected

ADORA1 (HGNC:262): (adenosine A1 receptor) The protein encoded by this gene is an adenosine receptor that belongs to the G-protein coupled receptor 1 family. There are 3 types of adenosine receptors, each with a specific pattern of ligand binding and tissue distribution, and together they regulate a diverse set of physiologic functions. The type A1 receptors inhibit adenylyl cyclase, and play a role in the fertilization process. Animal studies also suggest a role for A1 receptors in kidney function and ethanol intoxication. Transcript variants with alternative splicing in the 5' UTR have been found for this gene. [provided by RefSeq, Jul 2008]

ADORA1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP7

Synonymous conserved (PhyloP=-3.95 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADORA1	NM_000674.3 linkuse as main transcript	c.306T>G	p.Ala102=	synonymous_variant	3/4	ENST00000337894.9	NP_000665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADORA1	ENST00000337894.9 linkuse as main transcript	c.306T>G	p.Ala102=	synonymous_variant	3/4	2	NM_000674.3	ENSP00000338435	P1	P30542-1
ADORA1	ENST00000309502.7 linkuse as main transcript	c.306T>G	p.Ala102=	synonymous_variant	5/6	1		ENSP00000308549	P1	P30542-1
ADORA1	ENST00000367236.8 linkuse as main transcript	c.306T>G	p.Ala102=	synonymous_variant	2/3	1		ENSP00000356205	P1	P30542-1
ADORA1	ENST00000367235.1 linkuse as main transcript	c.306T>G	p.Ala102=	synonymous_variant	2/3	2		ENSP00000356204		P30542-2

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39814

AN:

152018

Hom.:

6008

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.273

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.391

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.257

GnomAD3 exomes

AF:

0.306

AC:

76837

AN:

250778

Hom.:

12676

AF XY:

0.317

AC XY:

43013

AN XY:

135490

show subpopulations

Gnomad AFR exome

AF:

0.118

Gnomad AMR exome

AF:

0.299

Gnomad ASJ exome

AF:

0.262

Gnomad EAS exome

AF:

0.149

Gnomad SAS exome

AF:

0.405

Gnomad FIN exome

AF:

0.339

Gnomad NFE exome

AF:

0.332

Gnomad OTH exome

AF:

0.300

GnomAD4 exome

AF:

0.323

AC:

472360

AN:

1461478

Hom.:

78750

Cov.:

AF XY:

0.327

AC XY:

237740

AN XY:

727006

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.295

Gnomad4 ASJ exome

AF:

0.258

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.409

Gnomad4 FIN exome

AF:

0.338

Gnomad4 NFE exome

AF:

0.332

Gnomad4 OTH exome

AF:

0.304

GnomAD4 genome

AF:

0.262

AC:

39831

AN:

152136

Hom.:

6012

Cov.:

AF XY:

0.263

AC XY:

19535

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.264

Gnomad4 ASJ

AF:

0.257

Gnomad4 EAS

AF:

0.148

Gnomad4 SAS

AF:

0.392

Gnomad4 FIN

AF:

0.337

Gnomad4 NFE

AF:

0.333

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.298

Hom.:

3167

Bravo

AF:

0.248

Asia WGS

AF:

0.259

AC:

900

AN:

3478

EpiCase

AF:

0.331

EpiControl

AF:

0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.1

DANN

Benign

0.47

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over