1-203165007-AT-ATT

Position:

• chr1-203165007-AT-ATT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000674.3(ADORA1):​c.342-250dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,541,912 control chromosomes in the GnomAD database, including 20,312 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (4941 hom., cov: 28)
  • Exomes 𝑓: 0.14 (15371 hom.)
• Consequence: ADORA1 NM_000674.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADORA1	NM_000674.3	c.342-250dupT		intron_variant		ENST00000337894.9	NP_000665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADORA1	ENST00000337894.9	c.342-250dupT		intron_variant		2	NM_000674.3	ENSP00000338435.4

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33237 AN: 151936 Hom.: 4931 Cov.: 28

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.206

GnomAD3 exomes AF: 0.158 AC: 23078 AN: 145850 Hom.: 2289 AF XY: 0.150 AC XY: 11743 AN XY: 78442

Gnomad AFR exome AF: 0.447

Gnomad AMR exome AF: 0.228

Gnomad ASJ exome AF: 0.165

Gnomad EAS exome AF: 0.153

Gnomad SAS exome AF: 0.113

Gnomad FIN exome AF: 0.114

Gnomad NFE exome AF: 0.124

Gnomad OTH exome AF: 0.160

GnomAD4 exome AF: 0.137 AC: 189940 AN: 1389858 Hom.: 15371 Cov.: 30 AF XY: 0.135 AC XY: 92323 AN XY: 685458

Gnomad4 AFR exome AF: 0.445

Gnomad4 AMR exome AF: 0.232

Gnomad4 ASJ exome AF: 0.161

Gnomad4 EAS exome AF: 0.178

Gnomad4 SAS exome AF: 0.114

Gnomad4 FIN exome AF: 0.112

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.164

GnomAD4 genome AF: 0.219 AC: 33281 AN: 152054 Hom.: 4941 Cov.: 28 AF XY: 0.215 AC XY: 16021 AN XY: 74344

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.204

Alfa AF: 0.166 Hom.: 490

Bravo AF: 0.240

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs5780149; hg19: chr1-203134135;