chr1-203166197-A-C

Position:

• chr1-203166197-A-C

Variant summary

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

The NM_000674.3(ADORA1):​c.*297A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.942 in 302,730 control chromosomes in the GnomAD database, including 134,512 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 0.94 (66893 hom., cov: 33)
  • Exomes 𝑓: 0.95 (67619 hom.)
• Consequence: ADORA1 NM_000674.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.13

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADORA1	NM_000674.3	c.*297A>C		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.*297A>C		3_prime_UTR_variant	4/4	2	NM_000674.3	ENSP00000338435	P1

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142453 AN: 152154 Hom.: 66852 Cov.: 33

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.983

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.922

GnomAD4 exome AF: 0.947 AC: 142505 AN: 150458 Hom.: 67619 Cov.: 3 AF XY: 0.947 AC XY: 71487 AN XY: 75480

Gnomad4 AFR exome AF: 0.912

Gnomad4 AMR exome AF: 0.837

Gnomad4 ASJ exome AF: 0.880

Gnomad4 EAS exome AF: 0.868

Gnomad4 SAS exome AF: 0.964

Gnomad4 FIN exome AF: 0.987

Gnomad4 NFE exome AF: 0.966

Gnomad4 OTH exome AF: 0.936

GnomAD4 genome AF: 0.936 AC: 142538 AN: 152272 Hom.: 66893 Cov.: 33 AF XY: 0.936 AC XY: 69667 AN XY: 74442

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.912

Alfa AF: 0.962 Hom.: 5427

Bravo AF: 0.922

Asia WGS AF: 0.868 AC: 3019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.010
DANN	Benign	0.65

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: rs6427994; hg19: chr1-203135325;