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
NM_006601.7 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.435
Publications
4 publications found
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 |
---|---|---|---|---|---|---|---|---|
PTGES3 | NM_006601.7 | c.2+1116_2+1117delAT | intron_variant | Intron 1 of 7 | ENST00000262033.11 | NP_006592.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGES3 | ENST00000262033.11 | c.2+1116_2+1117delAT | intron_variant | Intron 1 of 7 | 1 | NM_006601.7 | ENSP00000262033.6 | |||
PTGES3 | ENST00000456859.2 | c.2+1116_2+1117delAT | intron_variant | Intron 1 of 6 | 2 | ENSP00000389090.2 |
Frequencies
GnomAD3 genomes AF: 0.570 AC: 86094AN: 150976Hom.: 26293 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
86094
AN:
150976
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.639 AC: 157327AN: 246064Hom.: 50774 AF XY: 0.641 AC XY: 79939AN XY: 124668 show subpopulations
GnomAD4 exome
AF:
AC:
157327
AN:
246064
Hom.:
AF XY:
AC XY:
79939
AN XY:
124668
show subpopulations
African (AFR)
AF:
AC:
2369
AN:
7172
American (AMR)
AF:
AC:
4954
AN:
7428
Ashkenazi Jewish (ASJ)
AF:
AC:
5519
AN:
9232
East Asian (EAS)
AF:
AC:
15696
AN:
22880
South Asian (SAS)
AF:
AC:
2339
AN:
3030
European-Finnish (FIN)
AF:
AC:
14539
AN:
20796
Middle Eastern (MID)
AF:
AC:
783
AN:
1290
European-Non Finnish (NFE)
AF:
AC:
101066
AN:
157880
Other (OTH)
AF:
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: 86116AN: 151094Hom.: 26297 Cov.: 0 AF XY: 0.577 AC XY: 42572AN XY: 73718 show subpopulations
GnomAD4 genome
AF:
AC:
86116
AN:
151094
Hom.:
Cov.:
0
AF XY:
AC XY:
42572
AN XY:
73718
show subpopulations
African (AFR)
AF:
AC:
13780
AN:
41204
American (AMR)
AF:
AC:
10109
AN:
15060
Ashkenazi Jewish (ASJ)
AF:
AC:
2004
AN:
3470
East Asian (EAS)
AF:
AC:
3801
AN:
5122
South Asian (SAS)
AF:
AC:
3580
AN:
4800
European-Finnish (FIN)
AF:
AC:
7381
AN:
10374
Middle Eastern (MID)
AF:
AC:
169
AN:
294
European-Non Finnish (NFE)
AF:
AC:
43348
AN:
67774
Other (OTH)
AF:
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:
Hom.:
Bravo
AF:
Asia WGS
AF:
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:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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