3-151337866-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022788.5(P2RY12):c.980G>A(p.Arg327Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 152,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022788.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
P2RY12 | ENST00000302632.4 | c.980G>A | p.Arg327Lys | missense_variant | Exon 3 of 3 | 1 | NM_022788.5 | ENSP00000307259.4 | ||
MED12L | ENST00000687756.1 | c.2251-12193C>T | intron_variant | Intron 16 of 44 | NM_001393769.1 | ENSP00000508695.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1460982Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726814
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74244
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.980G>A (p.R327K) alteration is located in exon 3 (coding exon 1) of the P2RY12 gene. This alteration results from a G to A substitution at nucleotide position 980, causing the arginine (R) at amino acid position 327 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at