chr19-10113872-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002566.5(P2RY11):c.259G>A(p.Ala87Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,609,842 control chromosomes in the GnomAD database, including 15,102 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002566.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P2RY11 | NM_002566.5 | c.259G>A | p.Ala87Thr | missense_variant | 2/2 | ENST00000321826.5 | |
PPAN-P2RY11 | NM_001198690.2 | c.*18G>A | 3_prime_UTR_variant | 13/13 | |||
PPAN-P2RY11 | NM_001040664.3 | c.1519G>A | p.Ala507Thr | missense_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P2RY11 | ENST00000321826.5 | c.259G>A | p.Ala87Thr | missense_variant | 2/2 | 1 | NM_002566.5 | P1 | |
P2RY11 | ENST00000471843.1 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.131 AC: 19950AN: 152076Hom.: 1573 Cov.: 34
GnomAD3 exomes AF: 0.162 AC: 39430AN: 243908Hom.: 3988 AF XY: 0.160 AC XY: 21243AN XY: 132526
GnomAD4 exome AF: 0.127 AC: 185843AN: 1457646Hom.: 13524 Cov.: 37 AF XY: 0.129 AC XY: 93903AN XY: 725138
GnomAD4 genome AF: 0.131 AC: 19974AN: 152196Hom.: 1578 Cov.: 34 AF XY: 0.137 AC XY: 10179AN XY: 74422
ClinVar
Submissions by phenotype
P2RY11-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | 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