rs829259
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001104631.2(PDE4D):c.*2515A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,374 control chromosomes in the GnomAD database, including 26,301 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.59 ( 26217 hom., cov: 31)
Exomes 𝑓: 0.60 ( 84 hom. )
Consequence
PDE4D
NM_001104631.2 3_prime_UTR
NM_001104631.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.382
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 5-58972149-T-A is Benign according to our data. Variant chr5-58972149-T-A is described in ClinVar as [Benign]. Clinvar id is 353941.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE4D | NM_001104631.2 | c.*2515A>T | 3_prime_UTR_variant | 15/15 | ENST00000340635.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE4D | ENST00000340635.11 | c.*2515A>T | 3_prime_UTR_variant | 15/15 | 1 | NM_001104631.2 | |||
PDE4D | ENST00000507116.6 | c.*2515A>T | 3_prime_UTR_variant | 15/15 | 1 | P4 | |||
PDE4D | ENST00000636120.1 | c.*2515A>T | 3_prime_UTR_variant | 15/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.586 AC: 88938AN: 151828Hom.: 26203 Cov.: 31
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GnomAD4 exome AF: 0.598 AC: 256AN: 428Hom.: 84 Cov.: 0 AF XY: 0.569 AC XY: 148AN XY: 260
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GnomAD4 genome ? AF: 0.586 AC: 88989AN: 151946Hom.: 26217 Cov.: 31 AF XY: 0.584 AC XY: 43376AN XY: 74252
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Acrodysostosis 2 with or without hormone resistance Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at