Variant chr1-186673926-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000963.4(PTGS2):c.*427T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,406 control chromosomes in the GnomAD database, including 13,789 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as other (no stars).

Frequency

Genomes: 𝑓 0.40 ( 13771 hom., cov: 33)

Exomes 𝑓: 0.35 ( 18 hom. )

Consequence

PTGS2
NM_000963.4 3_prime_UTR

Scores

Clinical Significance

other no assertion criteria provided O:1

Conservation

PhyloP100: -1.15

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]

PTGS2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGS2	NM_000963.4 linkuse as main transcript	c.*427T>C		3_prime_UTR_variant	10/10	ENST00000367468.10

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
PTGS2	ENST00000367468.10 linkuse as main transcript	c.*427T>C	3_prime_UTR_variant	10/10	1	NM_000963.4	P1
PTGS2	ENST00000490885.6 linkuse as main transcript	n.2657T>C	non_coding_transcript_exon_variant	9/9	1
PTGS2	ENST00000680451.1 linkuse as main transcript	c.*427T>C	3_prime_UTR_variant	11/11			P1
PTGS2	ENST00000681605.1 linkuse as main transcript	c.*1914T>C	3_prime_UTR_variant, NMD_transcript_variant	10/10

Frequencies

GnomAD3 genomes

AF:

0.404

AC:

61413

AN:

151922

Hom.:

13726

Cov.:

show subpopulations

Gnomad AFR

AF:

0.607

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.319

Gnomad ASJ

AF:

0.336

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.391

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.287

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.365

GnomAD4 exome

AF:

0.347

AC:

127

AN:

366

Hom.:

Cov.:

AF XY:

0.357

AC XY:

AN XY:

224

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.341

Gnomad4 NFE exome

AF:

0.405

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.405

AC:

61514

AN:

152040

Hom.:

13771

Cov.:

AF XY:

0.398

AC XY:

29605

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.608

Gnomad4 AMR

AF:

0.319

Gnomad4 ASJ

AF:

0.336

Gnomad4 EAS

AF:

0.192

Gnomad4 SAS

AF:

0.392

Gnomad4 FIN

AF:

0.296

Gnomad4 NFE

AF:

0.341

Gnomad4 OTH

AF:

0.366

Alfa

AF:

0.350

Hom.:

13597

Bravo

AF:

0.412

Asia WGS

AF:

0.336

AC:

1165

AN:

3468

ClinVar

Significance: other

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Cholangiocarcinoma

Other:1

other, no assertion criteria provided

research

Department of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin Berlin

Dec 10, 2022

No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.96

DANN

Benign

0.38

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over