chr1-203099592-T-C

Position:

• chr1-203099592-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADORA1	ENST00000309502.7	c.-313+7882T>C		intron_variant		1		P1

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

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.316

Alfa AF: 0.331 Hom.: 3840

Bravo AF: 0.327

Asia WGS AF: 0.279 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.84

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: rs9660662; hg19: chr1-203068720;