dbSNP rs11315020: ADORA1:c.*814delT (chr1-203166712-CT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000674.3(ADORA1):c.*814delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.94 ( 66898 hom., cov: 0)

Exomes 𝑓: 0.95 ( 246 hom. )

Consequence

ADORA1
NM_000674.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

Publications

2 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

new If you want to explore the variant's impact on the transcript NM_000674.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000674.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADORA1	NM_000674.3	MANE Select	c.*814delT	3_prime_UTR	Exon 4 of 4	NP_000665.1	P30542-1
ADORA1	NM_001048230.2		c.*814delT	3_prime_UTR	Exon 3 of 3	NP_001041695.1	P30542-1
ADORA1	NM_001365065.1		c.*814delT	3_prime_UTR	Exon 3 of 3	NP_001351994.1	B7Z1L9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADORA1	ENST00000337894.9	TSL:2 MANE Select	c.*814delT	3_prime_UTR	Exon 4 of 4	ENSP00000338435.4	P30542-1
ADORA1	ENST00000309502.7	TSL:1	c.*814delT	3_prime_UTR	Exon 6 of 6	ENSP00000308549.3	P30542-1
ADORA1	ENST00000367236.8	TSL:1	c.*814delT	3_prime_UTR	Exon 3 of 3	ENSP00000356205.4	P30542-1

Frequencies

GnomAD3 genomes

AF:

0.936

AC:

142452

AN:

152140

Hom.:

66857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.918

Gnomad AMI

AF:

0.984

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:

0.923

GnomAD4 exome

AF:

0.950

AC:

513

AN:

540

Hom.:

246

Cov.:

AF XY:

0.946

AC XY:

384

AN XY:

406

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.875

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.714

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.966

AC:

456

AN:

472

Other (OTH)

AF:

0.850

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.936

AC:

142537

AN:

152258

Hom.:

66898

Cov.:

AF XY:

0.936

AC XY:

69662

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.918

AC:

38136

AN:

41548

American (AMR)

AF:

0.868

AC:

13286

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.871

AC:

3023

AN:

3472

East Asian (EAS)

AF:

0.796

AC:

4095

AN:

5144

South Asian (SAS)

AF:

0.962

AC:

4636

AN:

4820

European-Finnish (FIN)

AF:

0.988

AC:

10502

AN:

10628

Middle Eastern (MID)

AF:

0.871

AC:

256

AN:

294

European-Non Finnish (NFE)

AF:

0.967

AC:

65776

AN:

68026

Other (OTH)

AF:

0.913

AC:

1930

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

467

934

1402

1869

2336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

908

1816

2724

3632

4540

<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:

0.949

Hom.:

8358

Bravo

AF:

0.922

Asia WGS

AF:

0.867

AC:

3015

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over