rs876657424
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_170682.4(P2RX2):c.775-8_775-6delCTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00334 in 1,613,276 control chromosomes in the GnomAD database, including 183 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_170682.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0174 AC: 2637AN: 151414Hom.: 96 Cov.: 31
GnomAD3 exomes AF: 0.00443 AC: 1112AN: 251286Hom.: 21 AF XY: 0.00330 AC XY: 448AN XY: 135806
GnomAD4 exome AF: 0.00187 AC: 2739AN: 1461744Hom.: 87 AF XY: 0.00163 AC XY: 1186AN XY: 727198
GnomAD4 genome AF: 0.0175 AC: 2653AN: 151532Hom.: 96 Cov.: 31 AF XY: 0.0171 AC XY: 1267AN XY: 74012
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
c.775-11CTT[1] in intron 7 of P2RX2: This variant is not expected to have clinic al significance because it has been identified in 5.9% (614/10396) of African ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; dbSNP rs147087419). -
P2RX2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at