chr1-203125278-G-A

Position:

• chr1-203125278-G-A

Variant summary

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

The ENST00000665660.1(ENSG00000234775):​n.384+2529C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,060 control chromosomes in the GnomAD database, including 7,632 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 0.29 (7632 hom., cov: 32)
• Consequence: ENST00000665660.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADORA1	ENST00000309502.7	c.-312-2551G>A		intron_variant		1		ENSP00000308549	P1
	ENST00000665660.1	n.384+2529C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44407 AN: 151942 Hom.: 7623 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.292 AC: 44442 AN: 152060 Hom.: 7632 Cov.: 32 AF XY: 0.291 AC XY: 21599 AN XY: 74326

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.288

Alfa AF: 0.352 Hom.: 4767

Bravo AF: 0.271

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.9
DANN	Benign	0.70

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: rs1874142; hg19: chr1-203094406;