chr12-20369279-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000921.5(PDE3A):c.-6T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00327 in 1,508,492 control chromosomes in the GnomAD database, including 144 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.017 ( 84 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 60 hom. )
Consequence
PDE3A
NM_000921.5 5_prime_UTR
NM_000921.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.307
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 12-20369279-T-G is Benign according to our data. Variant chr12-20369279-T-G is described in ClinVar as [Benign]. Clinvar id is 3037518.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.058 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE3A | NM_000921.5 | c.-6T>G | 5_prime_UTR_variant | 1/16 | ENST00000359062.4 | ||
PDE3A | NM_001378407.1 | c.-6T>G | 5_prime_UTR_variant | 1/14 | |||
PDE3A | NM_001378408.1 | c.-1034T>G | 5_prime_UTR_variant | 1/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE3A | ENST00000359062.4 | c.-6T>G | 5_prime_UTR_variant | 1/16 | 1 | NM_000921.5 | P1 | ||
PDE3A-AS1 | ENST00000535755.1 | n.422+562A>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0171 AC: 2599AN: 151886Hom.: 84 Cov.: 32
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GnomAD3 exomes AF: 0.00390 AC: 452AN: 115798Hom.: 9 AF XY: 0.00323 AC XY: 197AN XY: 61076
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GnomAD4 exome AF: 0.00172 AC: 2331AN: 1356488Hom.: 60 Cov.: 32 AF XY: 0.00149 AC XY: 987AN XY: 663544
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GnomAD4 genome ? AF: 0.0171 AC: 2604AN: 152004Hom.: 84 Cov.: 32 AF XY: 0.0164 AC XY: 1221AN XY: 74270
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PDE3A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 07, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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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