1-203139380-T-C

Variant names:

• chr1-203139380-T-C
• rs10920573
• NM_000674.3:c.341+10198T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000674.3(ADORA1):​c.341+10198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,950 control chromosomes in the GnomAD database, including 21,087 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 0.50 (21087 hom., cov: 31)
• Consequence: ADORA1 NM_000674.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADORA1	NM_000674.3	c.341+10198T>C		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.341+10198T>C		intron_variant	Intron 3 of 3	2	NM_000674.3	ENSP00000338435.4

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76664 AN: 151832 Hom.: 21086 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.505 AC: 76668 AN: 151950 Hom.: 21087 Cov.: 31 AF XY: 0.504 AC XY: 37447 AN XY: 74272

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.518

Alfa AF: 0.564 Hom.: 6111

Bravo AF: 0.481

Asia WGS AF: 0.351 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.58

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: rs10920573; hg19: chr1-203108508; COSMIC: COSV58810930;