1-203166324-C-T

Position:

• chr1-203166324-C-T

Variant summary

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

The NM_000674.3(ADORA1):​c.*424C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0752 in 163,922 control chromosomes in the GnomAD database, including 767 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 0.077 (721 hom., cov: 33)
  • Exomes 𝑓: 0.057 (46 hom.)
• Consequence: ADORA1 NM_000674.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADORA1	NM_000674.3	c.*424C>T		3_prime_UTR_variant	4/4	ENST00000337894.9	NP_000665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADORA1	ENST00000337894.9	c.*424C>T		3_prime_UTR_variant	4/4	2	NM_000674.3	ENSP00000338435.4

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11660 AN: 151996 Hom.: 720 Cov.: 33

Gnomad AFR AF: 0.0974

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0674

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.0804

GnomAD4 exome AF: 0.0568 AC: 671 AN: 11806 Hom.: 46 Cov.: 0 AF XY: 0.0542 AC XY: 323 AN XY: 5958

Gnomad4 AFR exome AF: 0.0917

Gnomad4 AMR exome AF: 0.113

Gnomad4 ASJ exome AF: 0.0229

Gnomad4 EAS exome AF: 0.318

Gnomad4 SAS exome AF: 0.0893

Gnomad4 FIN exome AF: 0.0840

Gnomad4 NFE exome AF: 0.0389

Gnomad4 OTH exome AF: 0.0627

GnomAD4 genome AF: 0.0766 AC: 11659 AN: 152116 Hom.: 721 Cov.: 33 AF XY: 0.0815 AC XY: 6057 AN XY: 74364

Gnomad4 AFR AF: 0.0973

Gnomad4 AMR AF: 0.0971

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0674

Gnomad4 NFE AF: 0.0416

Gnomad4 OTH AF: 0.0791

Alfa AF: 0.0508 Hom.: 546

Bravo AF: 0.0806

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.77

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: rs16851030; hg19: chr1-203135452;