rs1874142

Variant names:

• chr1-203125278-G-A
• rs1874142
• ENST00000309502.7:c.-312-2551G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000309502.7(ADORA1):​c.-312-2551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,060 control chromosomes in the GnomAD database, including 7,632 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 0.29 (7632 hom., cov: 32)
• Consequence: ADORA1 ENST00000309502.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254
• Publications: 10 publications found

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]

ENSG00000234775 (HGNC:40066):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADORA1	ENST00000309502.7	c.-312-2551G>A		intron_variant	Intron 2 of 5	1		ENSP00000308549.3
ENSG00000234775	ENST00000665660.1	n.384+2529C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44407 AN: 151942 Hom.: 7623 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.292 AC: 44442 AN: 152060 Hom.: 7632 Cov.: 32 AF XY: 0.291 AC XY: 21599 AN XY: 74326

African (AFR) AF: 0.158 AC: 6547 AN: 41494

American (AMR) AF: 0.235 AC: 3588 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3470

East Asian (EAS) AF: 0.00541 AC: 28 AN: 5172

South Asian (SAS) AF: 0.271 AC: 1306 AN: 4824

European-Finnish (FIN) AF: 0.379 AC: 3997 AN: 10556

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26327 AN: 67958

Other (OTH) AF: 0.288 AC: 607 AN: 2110

Alfa AF: 0.342 Hom.: 20500

Bravo AF: 0.271

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.9
DANN	Benign	0.70
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1874142; hg19: chr1-203094406;