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. Variant got -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

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

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.657

Alfa AF: 0.659 Hom.: 30737

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

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: rs903361; hg19: chr1-203091274;