chr1-203166247-C-T

Position:

• chr1-203166247-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.*347C>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 0.0443 in 220,146 control chromosomes in the GnomAD database, including 275 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 0.041 (180 hom., cov: 33)
  • Exomes 𝑓: 0.052 (95 hom.)
• Consequence: ADORA1 NM_000674.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.068 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADORA1	NM_000674.3	c.*347C>T		3_prime_UTR_variant	4/4	ENST00000337894.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADORA1	ENST00000337894.9	c.*347C>T		3_prime_UTR_variant	4/4	2	NM_000674.3	P1

Frequencies

GnomAD3 genomes AF: 0.0409 AC: 6217 AN: 152122 Hom.: 179 Cov.: 33

Gnomad AFR AF: 0.00908

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0237

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0581

Gnomad OTH AF: 0.0383

GnomAD4 exome AF: 0.0522 AC: 3544 AN: 67906 Hom.: 95 Cov.: 0 AF XY: 0.0525 AC XY: 1792 AN XY: 34108

Gnomad4 AFR exome AF: 0.00988

Gnomad4 AMR exome AF: 0.0157

Gnomad4 ASJ exome AF: 0.0628

Gnomad4 EAS exome AF: 0.0348

Gnomad4 SAS exome AF: 0.0659

Gnomad4 FIN exome AF: 0.0662

Gnomad4 NFE exome AF: 0.0569

Gnomad4 OTH exome AF: 0.0440

GnomAD4 genome AF: 0.0408 AC: 6218 AN: 152240 Hom.: 180 Cov.: 33 AF XY: 0.0411 AC XY: 3061 AN XY: 74430

Gnomad4 AFR AF: 0.00905

Gnomad4 AMR AF: 0.0236

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.0245

Gnomad4 SAS AF: 0.0743

Gnomad4 FIN AF: 0.0703

Gnomad4 NFE AF: 0.0581

Gnomad4 OTH AF: 0.0379

Alfa AF: 0.0547 Hom.: 36

Bravo AF: 0.0339

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.14
DANN	Benign	0.71

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: rs41264025; hg19: chr1-203135375;