rs1778674
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001395426.1(PDE4DIP):c.20+7553A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 0)
Failed GnomAD Quality Control
Consequence
PDE4DIP
NM_001395426.1 intron
NM_001395426.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.545
Publications
3 publications found
Genes affected
PDE4DIP (HGNC:15580): (phosphodiesterase 4D interacting protein) The protein encoded by this gene serves to anchor phosphodiesterase 4D to the Golgi/centrosome region of the cell. Defects in this gene may be a cause of myeloproliferative disorder (MBD) associated with eosinophilia. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001395426.1. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PDE4DIP | NM_001395426.1 | MANE Select | c.20+7553A>G | intron | N/A | NP_001382355.1 | |||
| PDE4DIP | NM_001377392.2 | c.234-10903A>G | intron | N/A | NP_001364321.1 | ||||
| PDE4DIP | NM_001395298.1 | c.234-10903A>G | intron | N/A | NP_001382227.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PDE4DIP | ENST00000695795.1 | MANE Select | c.20+7553A>G | intron | N/A | ENSP00000512175.1 | |||
| PDE4DIP | ENST00000618462.4 | TSL:1 | c.20+7553A>G | intron | N/A | ENSP00000479409.1 | |||
| PDE4DIP | ENST00000530472.5 | TSL:1 | c.234-10903A>G | intron | N/A | ENSP00000482121.1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 174Hom.: 0 Cov.: 0
GnomAD3 genomes
AF:
AC:
0
AN:
174
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad NFE
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00 AC: 0AN: 174Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 100
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
174
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
100
African (AFR)
AF:
AC:
0
AN:
128
American (AMR)
AF:
AC:
0
AN:
6
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2
East Asian (EAS)
AF:
AC:
0
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
36
Other (OTH)
AC:
0
AN:
0
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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