chr12-132618993-CGCGGGGCGCGGGGT-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_170682.4(P2RX2):c.173+28_173+41del variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 1,150,744 control chromosomes in the GnomAD database, including 225,815 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.68 ( 30049 hom., cov: 0)
Exomes 𝑓: 0.61 ( 195766 hom. )
Consequence
P2RX2
NM_170682.4 splice_donor_5th_base, intron
NM_170682.4 splice_donor_5th_base, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.00
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 -16 ACMG points.
BP6
?
Variant 12-132618993-CGCGGGGCGCGGGGT-C is Benign according to our data. Variant chr12-132618993-CGCGGGGCGCGGGGT-C is described in ClinVar as [Benign]. Clinvar id is 508104.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RX2 | NM_170682.4 | c.173+28_173+41del | splice_donor_5th_base_variant, intron_variant | ENST00000643471.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RX2 | ENST00000643471.2 | c.173+28_173+41del | splice_donor_5th_base_variant, intron_variant | NM_170682.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.678 AC: 84084AN: 124046Hom.: 30002 Cov.: 0
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GnomAD3 exomes AF: 0.643 AC: 52932AN: 82320Hom.: 18709 AF XY: 0.629 AC XY: 29029AN XY: 46154
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GnomAD4 exome AF: 0.609 AC: 624741AN: 1026620Hom.: 195766 AF XY: 0.609 AC XY: 298151AN XY: 489498
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GnomAD4 genome ? AF: 0.678 AC: 84172AN: 124124Hom.: 30049 Cov.: 0 AF XY: 0.680 AC XY: 40363AN XY: 59342
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 12, 2018 | - - |
Autosomal dominant nonsyndromic hearing loss 41 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
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Name
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at