NM_000674.3:c.342-250dupT

Variant names:

• chr1-203165007-A-AT
• rs5780149
• NM_000674.3:c.342-250dupT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000674.3(ADORA1):​c.342-250dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,541,912 control chromosomes in the GnomAD database, including 20,312 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (4941 hom., cov: 28)
  • Exomes 𝑓: 0.14 (15371 hom.)
• Consequence: ADORA1 NM_000674.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 3 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA1	NM_000674.3	c.342-250dupT		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.342-254_342-253insT		intron_variant	Intron 3 of 3	2	NM_000674.3	ENSP00000338435.4

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33237 AN: 151936 Hom.: 4931 Cov.: 28

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.206

GnomAD2 exomes AF: 0.158 AC: 23078 AN: 145850 AF XY: 0.150

Gnomad AFR exome AF: 0.447

Gnomad AMR exome AF: 0.228

Gnomad ASJ exome AF: 0.165

Gnomad EAS exome AF: 0.153

Gnomad FIN exome AF: 0.114

Gnomad NFE exome AF: 0.124

Gnomad OTH exome AF: 0.160

GnomAD4 exome AF: 0.137 AC: 189940 AN: 1389858 Hom.: 15371 Cov.: 30 AF XY: 0.135 AC XY: 92323 AN XY: 685458

African (AFR) AF: 0.445 AC: 13865 AN: 31168

American (AMR) AF: 0.232 AC: 8065 AN: 34790

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 4035 AN: 25042

East Asian (EAS) AF: 0.178 AC: 6342 AN: 35654

South Asian (SAS) AF: 0.114 AC: 8865 AN: 78076

European-Finnish (FIN) AF: 0.112 AC: 5387 AN: 48142

Middle Eastern (MID) AF: 0.163 AC: 925 AN: 5668

European-Non Finnish (NFE) AF: 0.124 AC: 132991 AN: 1073636

Other (OTH) AF: 0.164 AC: 9465 AN: 57682

GnomAD4 genome AF: 0.219 AC: 33281 AN: 152054 Hom.: 4941 Cov.: 28 AF XY: 0.215 AC XY: 16021 AN XY: 74344

African (AFR) AF: 0.421 AC: 17444 AN: 41432

American (AMR) AF: 0.252 AC: 3852 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3468

East Asian (EAS) AF: 0.148 AC: 764 AN: 5172

South Asian (SAS) AF: 0.114 AC: 547 AN: 4814

European-Finnish (FIN) AF: 0.111 AC: 1174 AN: 10594

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8410 AN: 67978

Other (OTH) AF: 0.204 AC: 429 AN: 2108

Alfa AF: 0.166 Hom.: 490

Bravo AF: 0.240

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.22
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: rs5780149; hg19: chr1-203134135;