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GeneBe

rs5277

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_000963.4(PTGS2):c.306G>C(p.Val102=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,612,942 control chromosomes in the GnomAD database, including 17,422 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1296 hom., cov: 33)
Exomes 𝑓: 0.14 ( 16126 hom. )

Consequence

PTGS2
NM_000963.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420
Variant links:
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 -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP7
Synonymous conserved (PhyloP=0.042 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTGS2NM_000963.4 linkuse as main transcriptc.306G>C p.Val102= synonymous_variant 3/10 ENST00000367468.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTGS2ENST00000367468.10 linkuse as main transcriptc.306G>C p.Val102= synonymous_variant 3/101 NM_000963.4 P1

Frequencies

GnomAD3 genomes
AF:
0.114
AC:
17396
AN:
152120
Hom.:
1295
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0320
Gnomad AMI
AF:
0.0735
Gnomad AMR
AF:
0.124
Gnomad ASJ
AF:
0.109
Gnomad EAS
AF:
0.0371
Gnomad SAS
AF:
0.0785
Gnomad FIN
AF:
0.181
Gnomad MID
AF:
0.165
Gnomad NFE
AF:
0.161
Gnomad OTH
AF:
0.113
GnomAD3 exomes
AF:
0.120
AC:
29987
AN:
250388
Hom.:
2184
AF XY:
0.124
AC XY:
16736
AN XY:
135342
show subpopulations
Gnomad AFR exome
AF:
0.0302
Gnomad AMR exome
AF:
0.0784
Gnomad ASJ exome
AF:
0.105
Gnomad EAS exome
AF:
0.0392
Gnomad SAS exome
AF:
0.0820
Gnomad FIN exome
AF:
0.171
Gnomad NFE exome
AF:
0.159
Gnomad OTH exome
AF:
0.138
GnomAD4 exome
AF:
0.143
AC:
208553
AN:
1460704
Hom.:
16126
Cov.:
33
AF XY:
0.142
AC XY:
103113
AN XY:
726614
show subpopulations
Gnomad4 AFR exome
AF:
0.0274
Gnomad4 AMR exome
AF:
0.0812
Gnomad4 ASJ exome
AF:
0.107
Gnomad4 EAS exome
AF:
0.0377
Gnomad4 SAS exome
AF:
0.0835
Gnomad4 FIN exome
AF:
0.169
Gnomad4 NFE exome
AF:
0.157
Gnomad4 OTH exome
AF:
0.127
GnomAD4 genome
AF:
0.114
AC:
17389
AN:
152238
Hom.:
1296
Cov.:
33
AF XY:
0.114
AC XY:
8507
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.0318
Gnomad4 AMR
AF:
0.123
Gnomad4 ASJ
AF:
0.109
Gnomad4 EAS
AF:
0.0370
Gnomad4 SAS
AF:
0.0779
Gnomad4 FIN
AF:
0.181
Gnomad4 NFE
AF:
0.161
Gnomad4 OTH
AF:
0.114
Alfa
AF:
0.117
Hom.:
447
Bravo
AF:
0.105
Asia WGS
AF:
0.0780
AC:
270
AN:
3478
EpiCase
AF:
0.155
EpiControl
AF:
0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
Cadd
Benign
7.5
Dann
Benign
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5277; hg19: chr1-186648197; COSMIC: COSV66568541; COSMIC: COSV66568541; API