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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA1	NM_000674.3 link	c.*814delT		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.*814delT		3_prime_UTR_variant	Exon 4 of 4	2	NM_000674.3	ENSP00000338435.4		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

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

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 v4.3

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

Publications

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rs11315020

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