chr17-3898140-G-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002558.4(P2RX1):c.1033-30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0445 in 1,586,044 control chromosomes in the GnomAD database, including 1,888 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.033 ( 114 hom., cov: 30)
Exomes 𝑓: 0.046 ( 1774 hom. )
Consequence
P2RX1
NM_002558.4 intron
NM_002558.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0940
Genes affected
P2RX1 (HGNC:8533): (purinergic receptor P2X 1) The protein encoded by this gene belongs to the P2X family of G-protein-coupled receptors. These proteins can form homo-and heterotimers and function as ATP-gated ion channels and mediate rapid and selective permeability to cations. This protein is primarily localized to smooth muscle where binds ATP and mediates synaptic transmission between neurons and from neurons to smooth muscle and may being responsible for sympathetic vasoconstriction in small arteries, arterioles and vas deferens. Mouse studies suggest that this receptor is essential for normal male reproductive function. This protein may also be involved in promoting apoptosis. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 1 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 17-3898140-G-A is Benign according to our data. Variant chr17-3898140-G-A is described in ClinVar as [Benign]. Clinvar id is 1228110.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0619 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0332 AC: 5037AN: 151528Hom.: 115 Cov.: 30
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GnomAD3 exomes AF: 0.0385 AC: 9625AN: 250244Hom.: 272 AF XY: 0.0418 AC XY: 5666AN XY: 135428
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GnomAD4 exome AF: 0.0457 AC: 65520AN: 1434398Hom.: 1774 Cov.: 26 AF XY: 0.0472 AC XY: 33730AN XY: 715358
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GnomAD4 genome AF: 0.0332 AC: 5031AN: 151646Hom.: 114 Cov.: 30 AF XY: 0.0327 AC XY: 2420AN XY: 74074
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 21, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
BranchPoint Hunter
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at