chr1-186674413-G-T
Position:
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]
Genome browser will be placed here
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
GnomAD3 genomes
AF:
AC:
508
AN:
152172
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000855 AC: 215AN: 251460Hom.: 0 AF XY: 0.000662 AC XY: 90AN XY: 135904
GnomAD3 exomes
AF:
AC:
215
AN:
251460
Hom.:
AF XY:
AC XY:
90
AN XY:
135904
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000319 AC: 467AN: 1461694Hom.: 0 Cov.: 30 AF XY: 0.000257 AC XY: 187AN XY: 727164
GnomAD4 exome
AF:
AC:
467
AN:
1461694
Hom.:
Cov.:
30
AF XY:
AC XY:
187
AN XY:
727164
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00334 AC: 508AN: 152290Hom.: 1 Cov.: 33 AF XY: 0.00329 AC XY: 245AN XY: 74452
GnomAD4 genome
AF:
AC:
508
AN:
152290
Hom.:
Cov.:
33
AF XY:
AC XY:
245
AN XY:
74452
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 24, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at