Genetic Variant ADORA1:c.*347C>T (chr1-203166247-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000674.3(ADORA1):c.*347C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0443 in 220,146 control chromosomes in the GnomAD database, including 275 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 0.041 ( 180 hom., cov: 33)

Exomes 𝑓: 0.052 ( 95 hom. )

Consequence

ADORA1
NM_000674.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.20

Publications

7 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.068 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA1	NM_000674.3 link	c.*347C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000337894.9	NP_000665.1	P30542-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADORA1	ENST00000337894.9 link	c.*347C>T		3_prime_UTR_variant	Exon 4 of 4	2	NM_000674.3	ENSP00000338435.4		P30542-1

Frequencies

GnomAD3 genomes

AF:

0.0409

AC:

6217

AN:

152122

Hom.:

179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00908

Gnomad AMI

AF:

0.0351

Gnomad AMR

AF:

0.0237

Gnomad ASJ

AF:

0.0522

Gnomad EAS

AF:

0.0243

Gnomad SAS

AF:

0.0740

Gnomad FIN

AF:

0.0703

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0581

Gnomad OTH

AF:

0.0383

GnomAD4 exome

AF:

0.0522

AC:

3544

AN:

67906

Hom.:

Cov.:

AF XY:

0.0525

AC XY:

1792

AN XY:

34108

show subpopulations

African (AFR)

AF:

0.00988

AC:

AN:

2530

American (AMR)

AF:

0.0157

AC:

AN:

2108

Ashkenazi Jewish (ASJ)

AF:

0.0628

AC:

182

AN:

2898

East Asian (EAS)

AF:

0.0348

AC:

180

AN:

5170

South Asian (SAS)

AF:

0.0659

AC:

AN:

698

European-Finnish (FIN)

AF:

0.0662

AC:

297

AN:

4484

Middle Eastern (MID)

AF:

0.0519

AC:

AN:

366

European-Non Finnish (NFE)

AF:

0.0569

AC:

2554

AN:

44924

Other (OTH)

AF:

0.0440

AC:

208

AN:

4728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

163

327

490

654

817

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0408

AC:

6218

AN:

152240

Hom.:

180

Cov.:

AF XY:

0.0411

AC XY:

3061

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.00905

AC:

376

AN:

41548

American (AMR)

AF:

0.0236

AC:

361

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0522

AC:

181

AN:

3468

East Asian (EAS)

AF:

0.0245

AC:

127

AN:

5180

South Asian (SAS)

AF:

0.0743

AC:

358

AN:

4818

European-Finnish (FIN)

AF:

0.0703

AC:

746

AN:

10612

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0581

AC:

3950

AN:

68000

Other (OTH)

AF:

0.0379

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

309

617

926

1234

1543

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0547

Hom.:

Bravo

AF:

0.0339

Asia WGS

AF:

0.0490

AC:

171

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.14

(source)

DANN

Benign

0.71

PhyloP100

-2.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over