12-56671929-C-T

Variant summary

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

The NM_006601.7(PTGES3):​c.187-82G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 834,916 control chromosomes in the GnomAD database, including 194,710 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 0.70 ( 37276 hom., cov: 31)
Exomes 𝑓: 0.68 ( 157434 hom. )

Consequence

PTGES3
NM_006601.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.27
Variant links:
Genes affected
PTGES3 (HGNC:16049): (prostaglandin E synthase 3) This gene encodes an enzyme that converts prostaglandin endoperoxide H2 (PGH2) to prostaglandin E2 (PGE2). This protein functions as a co-chaperone with heat shock protein 90 (HSP90), localizing to response elements in DNA and disrupting transcriptional activation complexes. Alternative splicing results in multiple transcript variants. There are multiple pseudogenes of this gene on several different chromosomes. [provided by RefSeq, Feb 2016]

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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 (SAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PTGES3NM_006601.7 linkuse as main transcriptc.187-82G>A intron_variant ENST00000262033.11 NP_006592.3 Q15185-1A0A024RB32

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PTGES3ENST00000262033.11 linkuse as main transcriptc.187-82G>A intron_variant 1 NM_006601.7 ENSP00000262033.6 Q15185-1
PTGES3ENST00000456859.2 linkuse as main transcriptc.117-120G>A intron_variant 2 ENSP00000389090.2 B4DDC6

Frequencies

GnomAD3 genomes
AF:
0.699
AC:
106122
AN:
151864
Hom.:
37254
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.737
Gnomad AMI
AF:
0.759
Gnomad AMR
AF:
0.731
Gnomad ASJ
AF:
0.633
Gnomad EAS
AF:
0.744
Gnomad SAS
AF:
0.793
Gnomad FIN
AF:
0.718
Gnomad MID
AF:
0.639
Gnomad NFE
AF:
0.658
Gnomad OTH
AF:
0.697
GnomAD4 exome
AF:
0.677
AC:
462351
AN:
682934
Hom.:
157434
AF XY:
0.679
AC XY:
232254
AN XY:
342138
show subpopulations
Gnomad4 AFR exome
AF:
0.747
Gnomad4 AMR exome
AF:
0.752
Gnomad4 ASJ exome
AF:
0.654
Gnomad4 EAS exome
AF:
0.699
Gnomad4 SAS exome
AF:
0.796
Gnomad4 FIN exome
AF:
0.708
Gnomad4 NFE exome
AF:
0.664
Gnomad4 OTH exome
AF:
0.678
GnomAD4 genome
AF:
0.699
AC:
106197
AN:
151982
Hom.:
37276
Cov.:
31
AF XY:
0.703
AC XY:
52230
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.737
Gnomad4 AMR
AF:
0.731
Gnomad4 ASJ
AF:
0.633
Gnomad4 EAS
AF:
0.744
Gnomad4 SAS
AF:
0.792
Gnomad4 FIN
AF:
0.718
Gnomad4 NFE
AF:
0.658
Gnomad4 OTH
AF:
0.700
Alfa
AF:
0.669
Hom.:
40110
Bravo
AF:
0.699

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.2
DANN
Benign
0.37

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: rs2958154; hg19: chr12-57065713; API