rs149245

Positions:

• chr17-3676358-T-C
• chr17-3676358-T-G

Variant summary

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

The NM_002561.4(P2RX5):​c.1260-2481A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 984,580 control chromosomes in the GnomAD database, including 84,288 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 0.47 (18029 hom., cov: 32)
  • Exomes 𝑓: 0.40 (66259 hom.)
• Consequence: P2RX5 NM_002561.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

P2RX5 (HGNC:8536): (purinergic receptor P2X 5) The product of this gene belongs to the family of purinoceptors for ATP. This receptor functions as a ligand-gated ion channel. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the neighboring downstream gene, TAX1BP3 (Tax1 binding protein 3). [provided by RefSeq, Mar 2011]

P2RX5-TAX1BP3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
P2RX5	NM_002561.4	c.1260-2481A>G		intron_variant		ENST00000225328.10
P2RX5-TAX1BP3	NR_037928.1	n.1658+3232A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
P2RX5	ENST00000225328.10	c.1260-2481A>G		intron_variant		1	NM_002561.4

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71530 AN: 151934 Hom.: 18011 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.455

GnomAD4 exome AF: 0.396 AC: 330036 AN: 832528 Hom.: 66259 Cov.: 32 AF XY: 0.397 AC XY: 152702 AN XY: 384478

Gnomad4 AFR exome AF: 0.676

Gnomad4 AMR exome AF: 0.436

Gnomad4 ASJ exome AF: 0.419

Gnomad4 EAS exome AF: 0.556

Gnomad4 SAS exome AF: 0.464

Gnomad4 FIN exome AF: 0.311

Gnomad4 NFE exome AF: 0.387

Gnomad4 OTH exome AF: 0.428

GnomAD4 genome AF: 0.471 AC: 71604 AN: 152052 Hom.: 18029 Cov.: 32 AF XY: 0.468 AC XY: 34780 AN XY: 74328

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.457

Alfa AF: 0.390 Hom.: 2368

Bravo AF: 0.493

Asia WGS AF: 0.499 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.3
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs149245; hg19: chr17-3579652;