1-203129147-T-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000674.3(ADORA1):ā€‹c.306T>Gā€‹(p.Ala102=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,613,614 control chromosomes in the GnomAD database, including 84,762 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: š‘“ 0.26 ( 6012 hom., cov: 32)
Exomes š‘“: 0.32 ( 78750 hom. )

Consequence

ADORA1
NM_000674.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.95
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP7
Synonymous conserved (PhyloP=-3.95 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ADORA1NM_000674.3 linkuse as main transcriptc.306T>G p.Ala102= synonymous_variant 3/4 ENST00000337894.9 NP_000665.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADORA1ENST00000337894.9 linkuse as main transcriptc.306T>G p.Ala102= synonymous_variant 3/42 NM_000674.3 ENSP00000338435 P1P30542-1
ADORA1ENST00000309502.7 linkuse as main transcriptc.306T>G p.Ala102= synonymous_variant 5/61 ENSP00000308549 P1P30542-1
ADORA1ENST00000367236.8 linkuse as main transcriptc.306T>G p.Ala102= synonymous_variant 2/31 ENSP00000356205 P1P30542-1
ADORA1ENST00000367235.1 linkuse as main transcriptc.306T>G p.Ala102= synonymous_variant 2/32 ENSP00000356204 P30542-2

Frequencies

GnomAD3 genomes
AF:
0.262
AC:
39814
AN:
152018
Hom.:
6008
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.125
Gnomad AMI
AF:
0.273
Gnomad AMR
AF:
0.264
Gnomad ASJ
AF:
0.257
Gnomad EAS
AF:
0.148
Gnomad SAS
AF:
0.391
Gnomad FIN
AF:
0.337
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.333
Gnomad OTH
AF:
0.257
GnomAD3 exomes
AF:
0.306
AC:
76837
AN:
250778
Hom.:
12676
AF XY:
0.317
AC XY:
43013
AN XY:
135490
show subpopulations
Gnomad AFR exome
AF:
0.118
Gnomad AMR exome
AF:
0.299
Gnomad ASJ exome
AF:
0.262
Gnomad EAS exome
AF:
0.149
Gnomad SAS exome
AF:
0.405
Gnomad FIN exome
AF:
0.339
Gnomad NFE exome
AF:
0.332
Gnomad OTH exome
AF:
0.300
GnomAD4 exome
AF:
0.323
AC:
472360
AN:
1461478
Hom.:
78750
Cov.:
49
AF XY:
0.327
AC XY:
237740
AN XY:
727006
show subpopulations
Gnomad4 AFR exome
AF:
0.116
Gnomad4 AMR exome
AF:
0.295
Gnomad4 ASJ exome
AF:
0.258
Gnomad4 EAS exome
AF:
0.144
Gnomad4 SAS exome
AF:
0.409
Gnomad4 FIN exome
AF:
0.338
Gnomad4 NFE exome
AF:
0.332
Gnomad4 OTH exome
AF:
0.304
GnomAD4 genome
AF:
0.262
AC:
39831
AN:
152136
Hom.:
6012
Cov.:
32
AF XY:
0.263
AC XY:
19535
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.125
Gnomad4 AMR
AF:
0.264
Gnomad4 ASJ
AF:
0.257
Gnomad4 EAS
AF:
0.148
Gnomad4 SAS
AF:
0.392
Gnomad4 FIN
AF:
0.337
Gnomad4 NFE
AF:
0.333
Gnomad4 OTH
AF:
0.255
Alfa
AF:
0.298
Hom.:
3167
Bravo
AF:
0.248
Asia WGS
AF:
0.259
AC:
900
AN:
3478
EpiCase
AF:
0.331
EpiControl
AF:
0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
1.1
DANN
Benign
0.47

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2228079; hg19: chr1-203098275; COSMIC: COSV58809382; COSMIC: COSV58809382; API