chr1-203099592-T-C

Variant names:

• chr1-203099592-T-C
• rs9660662
• ENST00000309502.7:c.-313+7882T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000309502.7(ADORA1):​c.-313+7882T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,084 control chromosomes in the GnomAD database, including 8,443 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 0.33 (8443 hom., cov: 32)
• Consequence: ADORA1 ENST00000309502.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000309502.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADORA1	ENST00000309502.7	TSL:1	c.-313+7882T>C		intron	N/A	ENSP00000308549.3

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49919 AN: 151966 Hom.: 8422 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.329 AC: 49983 AN: 152084 Hom.: 8443 Cov.: 32 AF XY: 0.327 AC XY: 24298 AN XY: 74344

African (AFR) AF: 0.367 AC: 15202 AN: 41476

American (AMR) AF: 0.296 AC: 4527 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 946 AN: 3472

East Asian (EAS) AF: 0.150 AC: 778 AN: 5174

South Asian (SAS) AF: 0.390 AC: 1879 AN: 4820

European-Finnish (FIN) AF: 0.322 AC: 3401 AN: 10574

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22246 AN: 67974

Other (OTH) AF: 0.316 AC: 668 AN: 2114

Alfa AF: 0.330 Hom.: 4219

Bravo AF: 0.327

Asia WGS AF: 0.279 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		0.50
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: rs9660662; hg19: chr1-203068720;