rs702531
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001104631.2(PDE4D):c.*2768T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,336 control chromosomes in the GnomAD database, including 32,969 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.66 ( 32871 hom., cov: 31)
Exomes 𝑓: 0.65 ( 98 hom. )
Consequence
PDE4D
NM_001104631.2 3_prime_UTR
NM_001104631.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.47
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 5-58971896-A-C is Benign according to our data. Variant chr5-58971896-A-C is described in ClinVar as [Benign]. Clinvar id is 353937.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE4D | NM_001104631.2 | c.*2768T>G | 3_prime_UTR_variant | 15/15 | ENST00000340635.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE4D | ENST00000340635.11 | c.*2768T>G | 3_prime_UTR_variant | 15/15 | 1 | NM_001104631.2 | |||
PDE4D | ENST00000507116.6 | c.*2768T>G | 3_prime_UTR_variant | 15/15 | 1 | P4 | |||
PDE4D | ENST00000636120.1 | c.*2768T>G | 3_prime_UTR_variant | 15/15 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.657 AC: 99735AN: 151780Hom.: 32854 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
99735
AN:
151780
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.653 AC: 286AN: 438Hom.: 98 Cov.: 0 AF XY: 0.633 AC XY: 167AN XY: 264
GnomAD4 exome
AF:
AC:
286
AN:
438
Hom.:
Cov.:
0
AF XY:
AC XY:
167
AN XY:
264
Gnomad4 AFR exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.657 AC: 99793AN: 151898Hom.: 32871 Cov.: 31 AF XY: 0.654 AC XY: 48562AN XY: 74208
GnomAD4 genome
?
AF:
AC:
99793
AN:
151898
Hom.:
Cov.:
31
AF XY:
AC XY:
48562
AN XY:
74208
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
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 12, 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
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at