GeneBe

rs140759925

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000921.5(PDE3A):​c.-85_-74delTGTGTGTGTGTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000765 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: 0.0000059 ( 0 hom. )

Consequence

PDE3A
NM_000921.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.14
Variant links:
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]
PDE3A-AS1 (HGNC:40436): (PDE3A antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PDE3ANM_000921.5 linkc.-85_-74delTGTGTGTGTGTG 5_prime_UTR_variant Exon 1 of 16 ENST00000359062.4 NP_000912.3 Q14432
PDE3ANM_001378407.1 linkc.-85_-74delTGTGTGTGTGTG 5_prime_UTR_variant Exon 1 of 14 NP_001365336.1
PDE3ANM_001378408.1 linkc.-1113_-1102delTGTGTGTGTGTG 5_prime_UTR_variant Exon 1 of 18 NP_001365337.1
PDE3A-AS1NR_186033.1 linkn.416+639_416+650delACACACACACAC intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PDE3AENST00000359062 linkc.-85_-74delTGTGTGTGTGTG 5_prime_UTR_variant Exon 1 of 16 1 NM_000921.5 ENSP00000351957.3 Q14432
PDE3A-AS1ENST00000535755.1 linkn.422+639_422+650delACACACACACAC intron_variant Intron 1 of 1 4

Frequencies

GnomAD3 genomes
AF:
0.0000137
AC:
2
AN:
145556
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000683
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000505
GnomAD4 exome
AF:
0.00000591
AC:
3
AN:
508016
Hom.:
0
AF XY:
0.00000769
AC XY:
2
AN XY:
260156
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000611
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000741
GnomAD4 genome
AF:
0.0000137
AC:
2
AN:
145556
Hom.:
0
Cov.:
0
AF XY:
0.0000141
AC XY:
1
AN XY:
70756
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000683
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000505

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs140759925; hg19: chr12-20522124; API