12-56686880-CAT-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006601.7(PTGES3):​c.2+1116_2+1117delAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 397,158 control chromosomes in the GnomAD database, including 77,071 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.57 ( 26297 hom., cov: 0)
Exomes 𝑓: 0.64 ( 50774 hom. )

Consequence

PTGES3
NM_006601.7 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.435

Publications

4 publications found
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6
Variant 12-56686880-CAT-C is Benign according to our data. Variant chr12-56686880-CAT-C is described in ClinVar as Benign. ClinVar VariationId is 768555.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PTGES3NM_006601.7 linkc.2+1116_2+1117delAT intron_variant Intron 1 of 7 ENST00000262033.11 NP_006592.3 Q15185-1A0A024RB32

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PTGES3ENST00000262033.11 linkc.2+1116_2+1117delAT intron_variant Intron 1 of 7 1 NM_006601.7 ENSP00000262033.6 Q15185-1
PTGES3ENST00000456859.2 linkc.2+1116_2+1117delAT intron_variant Intron 1 of 6 2 ENSP00000389090.2 B4DDC6

Frequencies

GnomAD3 genomes
AF:
0.570
AC:
86094
AN:
150976
Hom.:
26293
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.335
Gnomad AMI
AF:
0.754
Gnomad AMR
AF:
0.671
Gnomad ASJ
AF:
0.578
Gnomad EAS
AF:
0.742
Gnomad SAS
AF:
0.746
Gnomad FIN
AF:
0.711
Gnomad MID
AF:
0.585
Gnomad NFE
AF:
0.640
Gnomad OTH
AF:
0.600
GnomAD4 exome
AF:
0.639
AC:
157327
AN:
246064
Hom.:
50774
AF XY:
0.641
AC XY:
79939
AN XY:
124668
show subpopulations
African (AFR)
AF:
0.330
AC:
2369
AN:
7172
American (AMR)
AF:
0.667
AC:
4954
AN:
7428
Ashkenazi Jewish (ASJ)
AF:
0.598
AC:
5519
AN:
9232
East Asian (EAS)
AF:
0.686
AC:
15696
AN:
22880
South Asian (SAS)
AF:
0.772
AC:
2339
AN:
3030
European-Finnish (FIN)
AF:
0.699
AC:
14539
AN:
20796
Middle Eastern (MID)
AF:
0.607
AC:
783
AN:
1290
European-Non Finnish (NFE)
AF:
0.640
AC:
101066
AN:
157880
Other (OTH)
AF:
0.615
AC:
10062
AN:
16356
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.460
Heterozygous variant carriers
0
2789
5577
8366
11154
13943
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
386
772
1158
1544
1930
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.570
AC:
86116
AN:
151094
Hom.:
26297
Cov.:
0
AF XY:
0.577
AC XY:
42572
AN XY:
73718
show subpopulations
African (AFR)
AF:
0.334
AC:
13780
AN:
41204
American (AMR)
AF:
0.671
AC:
10109
AN:
15060
Ashkenazi Jewish (ASJ)
AF:
0.578
AC:
2004
AN:
3470
East Asian (EAS)
AF:
0.742
AC:
3801
AN:
5122
South Asian (SAS)
AF:
0.746
AC:
3580
AN:
4800
European-Finnish (FIN)
AF:
0.711
AC:
7381
AN:
10374
Middle Eastern (MID)
AF:
0.575
AC:
169
AN:
294
European-Non Finnish (NFE)
AF:
0.640
AC:
43348
AN:
67774
Other (OTH)
AF:
0.604
AC:
1264
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1643
3286
4929
6572
8215
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
724
1448
2172
2896
3620
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.608
Hom.:
3605
Bravo
AF:
0.556
Asia WGS
AF:
0.732
AC:
2541
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.43
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.12
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs10579382; hg19: chr12-57080664; COSMIC: COSV107250840; API