dbSNP rs6427994: ADORA1:c.*297A>C (chr1-203166197-A-C) – 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.*297A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.942 in 302,730 control chromosomes in the GnomAD database, including 134,512 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 0.94 ( 66893 hom., cov: 33)

Exomes 𝑓: 0.95 ( 67619 hom. )

Consequence

ADORA1
NM_000674.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.13

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:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA1	NM_000674.3 link	c.*297A>C		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.*297A>C		3_prime_UTR_variant	Exon 4 of 4	2	NM_000674.3	ENSP00000338435.4		P30542-1

Frequencies

GnomAD3 genomes

AF:

0.936

AC:

142453

AN:

152154

Hom.:

66852

Cov.:

show subpopulations

Gnomad AFR

AF:

0.918

Gnomad AMI

AF:

0.983

Gnomad AMR

AF:

0.869

Gnomad ASJ

AF:

0.871

Gnomad EAS

AF:

0.797

Gnomad SAS

AF:

0.961

Gnomad FIN

AF:

0.988

Gnomad MID

AF:

0.858

Gnomad NFE

AF:

0.967

Gnomad OTH

AF:

0.922

GnomAD4 exome

AF:

0.947

AC:

142505

AN:

150458

Hom.:

67619

Cov.:

AF XY:

0.947

AC XY:

71487

AN XY:

75480

show subpopulations

African (AFR)

AF:

0.912

AC:

4635

AN:

5080

American (AMR)

AF:

0.837

AC:

4631

AN:

5534

Ashkenazi Jewish (ASJ)

AF:

0.880

AC:

5257

AN:

5974

East Asian (EAS)

AF:

0.868

AC:

10798

AN:

12442

South Asian (SAS)

AF:

0.964

AC:

2492

AN:

2586

European-Finnish (FIN)

AF:

0.987

AC:

10289

AN:

10422

Middle Eastern (MID)

AF:

0.919

AC:

765

AN:

832

European-Non Finnish (NFE)

AF:

0.966

AC:

94195

AN:

97498

Other (OTH)

AF:

0.936

AC:

9443

AN:

10090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

356

712

1068

1424

1780

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

382

764

1146

1528

1910

<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:

0.936

AC:

142538

AN:

152272

Hom.:

66893

Cov.:

AF XY:

0.936

AC XY:

69667

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.918

AC:

38117

AN:

41540

American (AMR)

AF:

0.868

AC:

13284

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.871

AC:

3021

AN:

3470

East Asian (EAS)

AF:

0.797

AC:

4117

AN:

5168

South Asian (SAS)

AF:

0.961

AC:

4639

AN:

4826

European-Finnish (FIN)

AF:

0.988

AC:

10494

AN:

10620

Middle Eastern (MID)

AF:

0.871

AC:

256

AN:

294

European-Non Finnish (NFE)

AF:

0.967

AC:

65787

AN:

68032

Other (OTH)

AF:

0.912

AC:

1930

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

471

942

1414

1885

2356

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

910

1820

2730

3640

4550

<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:

0.962

Hom.:

5427

Bravo

AF:

0.922

Asia WGS

AF:

0.868

AC:

3019

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.010

(source)

DANN

Benign

0.65

PhyloP100

-4.1

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