NM_000674.3:c.342-14898C>T

Variant names:

• chr1-203150363-C-T
• rs17511192
• NM_000674.3:c.342-14898C>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.342-14898C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,222 control chromosomes in the GnomAD database, including 10,043 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 0.32 (10043 hom., cov: 33)
• Consequence: ADORA1 NM_000674.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 14 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]

ENSG00000224671 (HGNC:40067):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA1	NM_000674.3	c.342-14898C>T		intron_variant	Intron 3 of 3	ENST00000337894.9	NP_000665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADORA1	ENST00000337894.9	c.342-14898C>T		intron_variant	Intron 3 of 3	2	NM_000674.3	ENSP00000338435.4

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48820 AN: 152104 Hom.: 10040 Cov.: 33

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.00615

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.350

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.321 AC: 48823 AN: 152222 Hom.: 10043 Cov.: 33 AF XY: 0.320 AC XY: 23818 AN XY: 74430

African (AFR) AF: 0.0923 AC: 3835 AN: 41556

American (AMR) AF: 0.290 AC: 4441 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1567 AN: 3470

East Asian (EAS) AF: 0.00617 AC: 32 AN: 5188

South Asian (SAS) AF: 0.270 AC: 1300 AN: 4822

European-Finnish (FIN) AF: 0.475 AC: 5028 AN: 10596

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31230 AN: 67980

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.420 Hom.: 22563

Bravo AF: 0.296

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.74
PhyloP100		-0.47
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: rs17511192; hg19: chr1-203119491;