rs1553638882
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PVS1_ModerateBP6_Moderate
The ENST00000369356.8(PDE4DIP):c.7053G>A(p.Trp2351Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000296 in 151,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00030 ( 0 hom., cov: 28)
Exomes 𝑓: 0.000034 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PDE4DIP
ENST00000369356.8 stop_gained
ENST00000369356.8 stop_gained
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 2.33
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 0 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.00508 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
BP6
Variant 1-149032053-G-A is Benign according to our data. Variant chr1-149032053-G-A is described in ClinVar as [Benign]. Clinvar id is 403293.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE4DIP | NM_001395426.1 | c.*68G>A | 3_prime_UTR_variant | 47/47 | ENST00000695795.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE4DIP | ENST00000695795.1 | c.*68G>A | 3_prime_UTR_variant | 47/47 | NM_001395426.1 |
Frequencies
GnomAD3 genomes AF: 0.000296 AC: 45AN: 151952Hom.: 0 Cov.: 28
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000343 AC: 50AN: 1457852Hom.: 0 Cov.: 31 AF XY: 0.0000290 AC XY: 21AN XY: 725146
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GnomAD4 genome AF: 0.000296 AC: 45AN: 151952Hom.: 0 Cov.: 28 AF XY: 0.000296 AC XY: 22AN XY: 74212
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency - |
Computational scores
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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