rs7314492
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_170682.4(P2RX2):c.-36T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 29)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
P2RX2
NM_170682.4 5_prime_UTR
NM_170682.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.465
Publications
6 publications found
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]
P2RX2 Gene-Disease associations (from GenCC):
- autosomal dominant nonsyndromic hearing loss 41Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- nonsyndromic genetic hearing lossInheritance: AD Classification: MODERATE Submitted by: ClinGen
- autosomal dominant nonsyndromic hearing lossInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 12-132618781-T-A is Benign according to our data. Variant chr12-132618781-T-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1194871.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_170682.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| P2RX2 | MANE Select | c.-36T>A | 5_prime_UTR | Exon 1 of 11 | ENSP00000494644.1 | Q9UBL9-1 | |||
| P2RX2 | TSL:1 | c.-36T>A | upstream_gene | N/A | ENSP00000343339.4 | Q9UBL9-4 | |||
| P2RX2 | TSL:1 | c.-36T>A | upstream_gene | N/A | ENSP00000343904.5 | Q9UBL9-3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
29
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1048578Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 497096
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1048578
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
497096
African (AFR)
AF:
AC:
0
AN:
21258
American (AMR)
AF:
AC:
0
AN:
6980
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
12034
East Asian (EAS)
AF:
AC:
0
AN:
22594
South Asian (SAS)
AF:
AC:
0
AN:
21108
European-Finnish (FIN)
AF:
AC:
0
AN:
27160
Middle Eastern (MID)
AF:
AC:
0
AN:
2904
European-Non Finnish (NFE)
AF:
AC:
0
AN:
894222
Other (OTH)
AF:
AC:
0
AN:
40318
GnomAD4 genome
GnomAD4 genome
Cov.:
29
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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