rs114276183
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_170682.4(P2RX2):c.1302G>A(p.Pro434=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00219 in 1,612,918 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.012 ( 29 hom., cov: 33)
Exomes 𝑓: 0.0012 ( 31 hom. )
Consequence
P2RX2
NM_170682.4 synonymous
NM_170682.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.47
Genes affected
P2RX2 (HGNC:15459): (purinergic receptor P2X 2) The product of this gene belongs to the family of purinoceptors for ATP. This receptor functions as a ligand-gated ion channel. Binding to ATP mediates synaptic transmission between neurons and from neurons to smooth muscle. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Aug 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 12-132621858-G-A is Benign according to our data. Variant chr12-132621858-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 226979.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.47 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0118 (1792/152222) while in subpopulation AFR AF= 0.0412 (1712/41536). AF 95% confidence interval is 0.0396. There are 29 homozygotes in gnomad4. There are 864 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1792 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RX2 | NM_170682.4 | c.1302G>A | p.Pro434= | synonymous_variant | 11/11 | ENST00000643471.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RX2 | ENST00000643471.2 | c.1302G>A | p.Pro434= | synonymous_variant | 11/11 | NM_170682.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0118 AC: 1792AN: 152104Hom.: 29 Cov.: 33
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GnomAD3 exomes AF: 0.00324 AC: 808AN: 249716Hom.: 13 AF XY: 0.00241 AC XY: 326AN XY: 135158
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GnomAD4 exome AF: 0.00119 AC: 1739AN: 1460696Hom.: 31 Cov.: 34 AF XY: 0.00102 AC XY: 743AN XY: 726670
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GnomAD4 genome ? AF: 0.0118 AC: 1792AN: 152222Hom.: 29 Cov.: 33 AF XY: 0.0116 AC XY: 864AN XY: 74442
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 09, 2016 | Pro460Pro in exon 10B of P2RX2: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 4.5% (463/10136) ( 178/4406) of African chromosomes by the Exome Aggregation Consortium (ExAC, http ://exac.broadinstitute.org; dbSNP rs114276183). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 17, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at