12-20369190-CGTGTGTGTGTGT-CGT
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_000921.5(PDE3A):c.-83_-74delTGTGTGTGTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000612 in 653,572 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000039 ( 0 hom. )
Consequence
PDE3A
NM_000921.5 5_prime_UTR
NM_000921.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.14
Publications
1 publications found
Genes affected
PDE3A (HGNC:8778): (phosphodiesterase 3A) This gene encodes a member of the cGMP-inhibited cyclic nucleotide phosphodiesterase (cGI-PDE) family. cGI-PDE enzymes hydrolyze both cAMP and cGMP, and play critical roles in many cellular processes by regulating the amplitude and duration of intracellular cyclic nucleotide signals. The encoded protein mediates platelet aggregation and also plays important roles in cardiovascular function by regulating vascular smooth muscle contraction and relaxation. Inhibitors of the encoded protein may be effective in treating congestive heart failure. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000921.5. 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 |
|---|---|---|---|---|---|---|---|---|---|
| PDE3A | NM_000921.5 | MANE Select | c.-83_-74delTGTGTGTGTG | 5_prime_UTR | Exon 1 of 16 | NP_000912.3 | |||
| PDE3A | NM_001378407.1 | c.-83_-74delTGTGTGTGTG | 5_prime_UTR | Exon 1 of 14 | NP_001365336.1 | ||||
| PDE3A | NM_001378408.1 | c.-1111_-1102delTGTGTGTGTG | 5_prime_UTR | Exon 1 of 18 | NP_001365337.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PDE3A | ENST00000359062.4 | TSL:1 MANE Select | c.-83_-74delTGTGTGTGTG | 5_prime_UTR | Exon 1 of 16 | ENSP00000351957.3 | Q14432 | ||
| PDE3A | ENST00000951762.1 | c.-83_-74delTGTGTGTGTG | 5_prime_UTR | Exon 1 of 15 | ENSP00000621821.1 | ||||
| PDE3A-AS1 | ENST00000535755.1 | TSL:4 | n.422+641_422+650delACACACACAC | intron | N/A |
Frequencies
GnomAD3 genomes 0.0000137 AC: 2AN: 145556Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
145556
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: 0.00000394 AC: 2AN: 508016Hom.: 0 AF XY: 0.00000769 AC XY: 2AN XY: 260158 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
508016
Hom.:
AF XY:
AC XY:
2
AN XY:
260158
show subpopulations
African (AFR)
AF:
AC:
0
AN:
12624
American (AMR)
AF:
AC:
0
AN:
16356
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
12868
East Asian (EAS)
AF:
AC:
0
AN:
27648
South Asian (SAS)
AF:
AC:
0
AN:
38632
European-Finnish (FIN)
AF:
AC:
0
AN:
30852
Middle Eastern (MID)
AF:
AC:
0
AN:
2094
European-Non Finnish (NFE)
AF:
AC:
2
AN:
339954
Other (OTH)
AF:
AC:
0
AN:
26988
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000137 AC: 2AN: 145556Hom.: 0 Cov.: 0 AF XY: 0.0000141 AC XY: 1AN XY: 70756 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
145556
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
70756
show subpopulations
African (AFR)
AF:
AC:
0
AN:
39778
American (AMR)
AF:
AC:
0
AN:
14634
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3406
East Asian (EAS)
AF:
AC:
0
AN:
4586
South Asian (SAS)
AF:
AC:
0
AN:
4528
European-Finnish (FIN)
AF:
AC:
0
AN:
9430
Middle Eastern (MID)
AF:
AC:
0
AN:
302
European-Non Finnish (NFE)
AF:
AC:
2
AN:
66050
Other (OTH)
AF:
AC:
0
AN:
1980
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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