rs903361

Variant names:

• chr1-203122146-G-A
• rs903361
• ENST00000309502.7:c.-312-5683G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-203122146-G-A
• chr1-203122146-G-C

Variant summary

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

The ENST00000309502.7(ADORA1):​c.-312-5683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,070 control chromosomes in the GnomAD database, including 32,562 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 0.65 (32562 hom., cov: 32)
• Consequence: ADORA1 ENST00000309502.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 25 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.676 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.-312-5683G>A		intron_variant	Intron 2 of 5	1		ENSP00000308549.3
ENSG00000234775	ENST00000665660.1	n.385-4244C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99278 AN: 151952 Hom.: 32551 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.653 AC: 99322 AN: 152070 Hom.: 32562 Cov.: 32 AF XY: 0.652 AC XY: 48457 AN XY: 74344

African (AFR) AF: 0.654 AC: 27085 AN: 41438

American (AMR) AF: 0.687 AC: 10502 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2294 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3193 AN: 5170

South Asian (SAS) AF: 0.491 AC: 2368 AN: 4822

European-Finnish (FIN) AF: 0.661 AC: 6997 AN: 10588

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44645 AN: 67982

Other (OTH) AF: 0.657 AC: 1388 AN: 2114

Alfa AF: 0.661 Hom.: 83989

Bravo AF: 0.658

Asia WGS AF: 0.579 AC: 2013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.73
PhyloP100		-0.34
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: rs903361; hg19: chr1-203091274;