rs3218625
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000963.4(PTGS2):c.1759G>A(p.Gly587Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000491 in 1,613,804 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000963.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTGS2 | NM_000963.4 | c.1759G>A | p.Gly587Arg | missense_variant | 10/10 | ENST00000367468.10 | NP_000954.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGS2 | ENST00000367468.10 | c.1759G>A | p.Gly587Arg | missense_variant | 10/10 | 1 | NM_000963.4 | ENSP00000356438.5 |
Frequencies
GnomAD3 genomes AF: 0.000645 AC: 98AN: 152008Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00163 AC: 409AN: 251448Hom.: 3 AF XY: 0.00146 AC XY: 199AN XY: 135898
GnomAD4 exome AF: 0.000475 AC: 695AN: 1461678Hom.: 4 Cov.: 30 AF XY: 0.000441 AC XY: 321AN XY: 727150
GnomAD4 genome AF: 0.000644 AC: 98AN: 152126Hom.: 1 Cov.: 33 AF XY: 0.000726 AC XY: 54AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at