NM_002599.5:c.1500C>G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_002599.5(PDE2A):c.1500C>G(p.Arg500Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
PDE2A
NM_002599.5 synonymous
NM_002599.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0340
Publications
0 publications found
Genes affected
PDE2A (HGNC:8777): (phosphodiesterase 2A) Enables several functions, including 3',5'-cyclic-nucleotide phosphodiesterase activity; anion binding activity; and metal ion binding activity. Involved in several processes, including cellular response to organic cyclic compound; cyclic-nucleotide-mediated signaling; and regulation of vascular permeability. Located in several cellular components, including cytosol; mitochondrial membrane; and perinuclear region of cytoplasm. Colocalizes with plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 11-72584588-G-C is Benign according to our data. Variant chr11-72584588-G-C is described in ClinVar as Likely_benign. ClinVar VariationId is 1667178.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.034 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002599.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PDE2A | MANE Select | c.1500C>G | p.Arg500Arg | synonymous | Exon 18 of 31 | NP_002590.1 | O00408-1 | ||
| PDE2A | c.1479C>G | p.Arg493Arg | synonymous | Exon 17 of 30 | NP_001137311.1 | O00408-3 | |||
| PDE2A | c.1473C>G | p.Arg491Arg | synonymous | Exon 19 of 32 | NP_001139681.1 | O00408-4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PDE2A | TSL:1 MANE Select | c.1500C>G | p.Arg500Arg | synonymous | Exon 18 of 31 | ENSP00000334910.5 | O00408-1 | ||
| PDE2A | TSL:1 | c.1473C>G | p.Arg491Arg | synonymous | Exon 19 of 32 | ENSP00000446399.1 | O00408-4 | ||
| PDE2A | TSL:5 | c.1479C>G | p.Arg493Arg | synonymous | Exon 17 of 30 | ENSP00000442256.1 | O00408-3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460048Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 726394 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1460048
Hom.:
Cov.:
34
AF XY:
AC XY:
0
AN XY:
726394
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33472
American (AMR)
AF:
AC:
0
AN:
44700
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26122
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86222
European-Finnish (FIN)
AF:
AC:
0
AN:
51772
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111936
Other (OTH)
AF:
AC:
0
AN:
60358
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
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55-60
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
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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