Genetic Variant ADORA1:c.*424C>T (chr1-203166324-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.*424C>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 0.0752 in 163,922 control chromosomes in the GnomAD database, including 767 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 0.077 ( 721 hom., cov: 33)

Exomes 𝑓: 0.057 ( 46 hom. )

Consequence

ADORA1
NM_000674.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15

Publications

15 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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA1	NM_000674.3 link	c.*424C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000337894.9	NP_000665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADORA1	ENST00000337894.9 link	c.*424C>T		3_prime_UTR_variant	Exon 4 of 4	2	NM_000674.3	ENSP00000338435.4

Frequencies

GnomAD3 genomes

AF:

0.0767

AC:

11660

AN:

151996

Hom.:

720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0974

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.0974

Gnomad ASJ

AF:

0.0207

Gnomad EAS

AF:

0.357

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.0674

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0416

Gnomad OTH

AF:

0.0804

GnomAD4 exome

AF:

0.0568

AC:

671

AN:

11806

Hom.:

Cov.:

AF XY:

0.0542

AC XY:

323

AN XY:

5958

show subpopulations

African (AFR)

AF:

0.0917

AC:

AN:

458

American (AMR)

AF:

0.113

AC:

AN:

450

Ashkenazi Jewish (ASJ)

AF:

0.0229

AC:

AN:

480

East Asian (EAS)

AF:

0.318

AC:

124

AN:

390

South Asian (SAS)

AF:

0.0893

AC:

AN:

168

European-Finnish (FIN)

AF:

0.0840

AC:

AN:

500

Middle Eastern (MID)

AF:

0.105

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0389

AC:

332

AN:

8524

Other (OTH)

AF:

0.0627

AC:

AN:

798

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

116

145

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0766

AC:

11659

AN:

152116

Hom.:

721

Cov.:

AF XY:

0.0815

AC XY:

6057

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0973

AC:

4037

AN:

41476

American (AMR)

AF:

0.0971

AC:

1486

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0207

AC:

AN:

3472

East Asian (EAS)

AF:

0.357

AC:

1836

AN:

5148

South Asian (SAS)

AF:

0.101

AC:

489

AN:

4820

European-Finnish (FIN)

AF:

0.0674

AC:

713

AN:

10586

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0416

AC:

2829

AN:

68000

Other (OTH)

AF:

0.0791

AC:

167

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

512

1025

1537

2050

2562

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

130

260

390

520

650

<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:

0.0561

Hom.:

1659

Bravo

AF:

0.0806

Asia WGS

AF:

0.199

AC:

694

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

1.1

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