dbSNP rs4648291: PTGS2:c.*277_*281delTTATA (chr1-186674071-TTATAA-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000963.4(PTGS2):c.*277_*281delTTATA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 171,644 control chromosomes in the GnomAD database, including 3,165 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 3109 hom., cov: 31)

Exomes 𝑓: 0.019 ( 56 hom. )

Consequence

PTGS2
NM_000963.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGS2	NM_000963.4 link	c.277_281delTTATA		3_prime_UTR_variant	Exon 10 of 10	ENST00000367468.10	NP_000954.1	P35354

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGS2	ENST00000367468 link	c.277_281delTTATA		3_prime_UTR_variant	Exon 10 of 10	1	NM_000963.4	ENSP00000356438.5		P35354

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17211

AN:

151872

Hom.:

3088

Cov.:

show subpopulations

Gnomad AFR

AF:

0.390

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0430

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0375

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.00187

Gnomad OTH

AF:

0.0843

GnomAD4 exome

AF:

0.0187

AC:

368

AN:

19654

Hom.:

AF XY:

0.0158

AC XY:

170

AN XY:

10738

show subpopulations

Gnomad4 AFR exome

AF:

0.402

Gnomad4 AMR exome

AF:

0.0297

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000650

Gnomad4 SAS exome

AF:

0.0490

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00157

Gnomad4 OTH exome

AF:

0.0439

GnomAD4 genome

AF:

0.114

AC:

17271

AN:

151990

Hom.:

3109

Cov.:

AF XY:

0.110

AC XY:

8151

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.390

Gnomad4 AMR

AF:

0.0430

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.000770

Gnomad4 SAS

AF:

0.0369

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00185

Gnomad4 OTH

AF:

0.0834

Alfa

AF:

0.0938

Hom.:

256

Bravo

AF:

0.130

Asia WGS

AF:

0.0430

AC:

150

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over