rs918590
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000502484.6(PDE4D):c.-90+85961T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,072 control chromosomes in the GnomAD database, including 8,695 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.32 ( 8695 hom., cov: 32)
Consequence
PDE4D
ENST00000502484.6 intron
ENST00000502484.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.104
Genes affected
PDE4D (HGNC:8783): (phosphodiesterase 4D) This gene encodes one of four mammalian counterparts to the fruit fly 'dunce' gene. The encoded protein has 3',5'-cyclic-AMP phosphodiesterase activity and degrades cAMP, which acts as a signal transduction molecule in multiple cell types. This gene uses different promoters to generate multiple alternatively spliced transcript variants that encode functional proteins.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDE4D | NM_001165899.2 | c.-90+85961T>G | intron_variant | NP_001159371.1 | ||||
PDE4D | NM_001349241.2 | c.-193+85961T>G | intron_variant | NP_001336170.1 | ||||
PDE4D | NM_001349243.2 | c.-674+85961T>G | intron_variant | NP_001336172.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDE4D | ENST00000502484.6 | c.-90+85961T>G | intron_variant | 1 | ENSP00000423094 | |||||
PDE4D | ENST00000509355.5 | n.157+85961T>G | intron_variant, non_coding_transcript_variant | 1 | ||||||
PDE4D | ENST00000505507.6 | c.-213+85961T>G | intron_variant | 4 | ENSP00000425910 |
Frequencies
GnomAD3 genomes AF: 0.316 AC: 47956AN: 151954Hom.: 8678 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.316 AC: 47999AN: 152072Hom.: 8695 Cov.: 32 AF XY: 0.316 AC XY: 23456AN XY: 74340
GnomAD4 genome
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1846
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at