rs10920569

chr1-203129327-T-C

Variant summary

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

The NM_000674.3(ADORA1):c.341+145T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 1,430,822 control chromosomes in the GnomAD database, including 74,794 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 0.26 (5944 hom., cov: 33)
  • Exomes 𝑓: 0.32 (68850 hom.)
• Consequence: ADORA1 NM_000674.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

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]

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 (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADORA1	NM_000674.3	c.341+145T>C		intron_variant		ENST00000337894.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADORA1	ENST00000337894.9	c.341+145T>C		intron_variant		2	NM_000674.3	P1
ADORA1	ENST00000309502.7	c.341+145T>C		intron_variant		1		P1
ADORA1	ENST00000367236.8	c.341+145T>C		intron_variant		1		P1
ADORA1	ENST00000367235.1	c.341+145T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39193 AN: 152076 Hom.: 5941 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.323 AC: 413194 AN: 1278628 Hom.: 68850 AF XY: 0.326 AC XY: 202998 AN XY: 621946

Gnomad4 AFR exome AF: 0.0971

Gnomad4 AMR exome AF: 0.284

Gnomad4 ASJ exome AF: 0.259

Gnomad4 EAS exome AF: 0.145

Gnomad4 SAS exome AF: 0.410

Gnomad4 FIN exome AF: 0.337

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.303

GnomAD4 genome AF: 0.258 AC: 39207 AN: 152194 Hom.: 5944 Cov.: 33 AF XY: 0.259 AC XY: 19248 AN XY: 74394

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.253

Alfa AF: 0.319 Hom.: 4025

Bravo AF: 0.243

Asia WGS AF: 0.256 AC: 889 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	6.3
Dann	Benign	0.70

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: rs10920569; hg19: chr1-203098455;