chr12-20369530-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_000921.5(PDE3A):c.246C>T(p.Arg82=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000578 in 1,557,898 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: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000058 ( 0 hom. )
Consequence
PDE3A
NM_000921.5 synonymous
NM_000921.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.95
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 made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
?
Variant 12-20369530-C-T is Benign according to our data. Variant chr12-20369530-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2046242.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.95 with no splicing effect.
BS2
?
High AC in GnomAd at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE3A | NM_000921.5 | c.246C>T | p.Arg82= | synonymous_variant | 1/16 | ENST00000359062.4 | |
PDE3A | NM_001378407.1 | c.246C>T | p.Arg82= | synonymous_variant | 1/14 | ||
PDE3A | NM_001378408.1 | c.-783C>T | 5_prime_UTR_variant | 1/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE3A | ENST00000359062.4 | c.246C>T | p.Arg82= | synonymous_variant | 1/16 | 1 | NM_000921.5 | P1 | |
PDE3A-AS1 | ENST00000535755.1 | n.422+311G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152140Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000144 AC: 23AN: 159894Hom.: 0 AF XY: 0.000152 AC XY: 13AN XY: 85704
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GnomAD4 exome AF: 0.0000576 AC: 81AN: 1405758Hom.: 0 Cov.: 34 AF XY: 0.0000533 AC XY: 37AN XY: 693836
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GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74320
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at