1-148953147-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP4
The NM_001395426.1(PDE4DIP):c.835-7507G>A variant causes a intron change. The variant allele was found at a frequency of 0.0000161 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
PDE4DIP
NM_001395426.1 intron
NM_001395426.1 intron
Scores
2
5
Clinical Significance
Conservation
PhyloP100: 3.85
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 made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-148953147-G-A is Pathogenic according to our data. Variant chr1-148953147-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 1174534.Status of the report is criteria_provided_single_submitter, 1 stars.
BP4
Computational evidence support a benign effect (MetaRNN=0.12463787). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDE4DIP | NM_001395426.1 | c.835-7507G>A | intron_variant | ENST00000695795.1 | NP_001382355.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDE4DIP | ENST00000695795.1 | c.835-7507G>A | intron_variant | NM_001395426.1 | ENSP00000512175 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251490Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135918
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GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727230
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74326
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
See cases Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Mani Lab, Yale Cardiovascular Research Center, Yale University | Jun 01, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
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Benign
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Uncertain
LIST_S2
Benign
T;T
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Benign
T;T
PROVEAN
Benign
N;N
Sift
Benign
T;T
Sift4G
Uncertain
T;D
Vest4
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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