rs3766566

Positions:

• chr1-203136227-G-A
• chr1-203136227-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000674.3(ADORA1):​c.341+7045G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,096 control chromosomes in the GnomAD database, including 3,241 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 0.20 (3241 hom., cov: 32)
• Consequence: ADORA1 NM_000674.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.35

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADORA1	NM_000674.3	c.341+7045G>A		intron_variant		ENST00000337894.9	NP_000665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADORA1	ENST00000337894.9	c.341+7045G>A		intron_variant		2	NM_000674.3	ENSP00000338435.4

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29857 AN: 151978 Hom.: 3243 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.216

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.196 AC: 29844 AN: 152096 Hom.: 3241 Cov.: 32 AF XY: 0.197 AC XY: 14676 AN XY: 74326

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.213

Alfa AF: 0.200 Hom.: 2551

Bravo AF: 0.196

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.42

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

Other links and lift over

dbSNP: rs3766566; hg19: chr1-203105355;