chr1-186674413-G-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000963.4(PTGS2):c.1755C>A(p.Arg585=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000604 in 1,613,984 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0033 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00032 ( 0 hom. )
Consequence
PTGS2
NM_000963.4 synonymous
NM_000963.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.803
Genes affected
PTGS2 (HGNC:9605): (prostaglandin-endoperoxide synthase 2) Prostaglandin-endoperoxide synthase (PTGS), also known as cyclooxygenase, is the key enzyme in prostaglandin biosynthesis, and acts both as a dioxygenase and as a peroxidase. There are two isozymes of PTGS: a constitutive PTGS1 and an inducible PTGS2, which differ in their regulation of expression and tissue distribution. This gene encodes the inducible isozyme. It is regulated by specific stimulatory events, suggesting that it is responsible for the prostanoid biosynthesis involved in inflammation and mitogenesis. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 1-186674413-G-T is Benign according to our data. Variant chr1-186674413-G-T is described in ClinVar as [Benign]. Clinvar id is 720903.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.803 with no splicing effect.
BS2
High AC in GnomAd4 at 508 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGS2 | NM_000963.4 | c.1755C>A | p.Arg585= | synonymous_variant | 10/10 | ENST00000367468.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGS2 | ENST00000367468.10 | c.1755C>A | p.Arg585= | synonymous_variant | 10/10 | 1 | NM_000963.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00334 AC: 508AN: 152172Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000855 AC: 215AN: 251460Hom.: 0 AF XY: 0.000662 AC XY: 90AN XY: 135904
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GnomAD4 exome AF: 0.000319 AC: 467AN: 1461694Hom.: 0 Cov.: 30 AF XY: 0.000257 AC XY: 187AN XY: 727164
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GnomAD4 genome AF: 0.00334 AC: 508AN: 152290Hom.: 1 Cov.: 33 AF XY: 0.00329 AC XY: 245AN XY: 74452
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Apr 24, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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