1-203166324-C-T

Variant names:

• chr1-203166324-C-T
• rs16851030
• NM_000674.3:c.*424C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000674.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADORA1	NM_000674.3	MANE Select	c.*424C>T		3_prime_UTR	Exon 4 of 4	NP_000665.1
	ADORA1	NM_001048230.2		c.*424C>T		3_prime_UTR	Exon 3 of 3	NP_001041695.1
	ADORA1	NM_001365065.1		c.*424C>T		3_prime_UTR	Exon 3 of 3	NP_001351994.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADORA1	ENST00000337894.9	TSL:2 MANE Select	c.*424C>T		3_prime_UTR	Exon 4 of 4	ENSP00000338435.4
	ADORA1	ENST00000309502.7	TSL:1	c.*424C>T		3_prime_UTR	Exon 6 of 6	ENSP00000308549.3
	ADORA1	ENST00000367236.8	TSL:1	c.*424C>T		3_prime_UTR	Exon 3 of 3	ENSP00000356205.4

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

African (AFR) AF: 0.0917 AC: 42 AN: 458

American (AMR) AF: 0.113 AC: 51 AN: 450

Ashkenazi Jewish (ASJ) AF: 0.0229 AC: 11 AN: 480

East Asian (EAS) AF: 0.318 AC: 124 AN: 390

South Asian (SAS) AF: 0.0893 AC: 15 AN: 168

European-Finnish (FIN) AF: 0.0840 AC: 42 AN: 500

Middle Eastern (MID) AF: 0.105 AC: 4 AN: 38

European-Non Finnish (NFE) AF: 0.0389 AC: 332 AN: 8524

Other (OTH) AF: 0.0627 AC: 50 AN: 798

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

African (AFR) AF: 0.0973 AC: 4037 AN: 41476

American (AMR) AF: 0.0971 AC: 1486 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3472

East Asian (EAS) AF: 0.357 AC: 1836 AN: 5148

South Asian (SAS) AF: 0.101 AC: 489 AN: 4820

European-Finnish (FIN) AF: 0.0674 AC: 713 AN: 10586

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0416 AC: 2829 AN: 68000

Other (OTH) AF: 0.0791 AC: 167 AN: 2112

Alfa AF: 0.0561 Hom.: 1659

Bravo AF: 0.0806

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.77
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16851030; hg19: chr1-203135452;