NM_001395426.1:c.927delA

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001395426.1(PDE4DIP):c.927delA(p.Glu309AspfsTer23) variant causes a frameshift change. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00044 ( 0 hom., cov: 17)

Exomes 𝑓: 0.0058 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PDE4DIP
NM_001395426.1 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.95

Publications

25 publications found

Variant links:

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]

PDE4DIP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP6

Variant 1-148960744-GA-G is Benign according to our data. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-148960744-GA-G is described in CliVar as Benign. Clinvar id is 403294.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE4DIP	NM_001395426.1 link	c.927delA	p.Glu309AspfsTer23	frameshift_variant	Exon 9 of 47	ENST00000695795.1	NP_001382355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE4DIP	ENST00000695795.1 link	c.927delA	p.Glu309AspfsTer23	frameshift_variant	Exon 9 of 47		NM_001395426.1	ENSP00000512175.1		A0A8Q3SI83

Frequencies

GnomAD3 genomes

AF:

0.000450

AC:

AN:

122224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000608

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000361

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00346

Gnomad SAS

AF:

0.000952

Gnomad FIN

AF:

0.000389

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000501

Gnomad OTH

AF:

0.000650

GnomAD2 exomes

AF:

0.173

AC:

40004

AN:

231748

AF XY:

0.171

show subpopulations

Gnomad AFR exome

AF:

0.0296

Gnomad AMR exome

AF:

0.238

Gnomad ASJ exome

AF:

0.0919

Gnomad EAS exome

AF:

0.381

Gnomad FIN exome

AF:

0.200

Gnomad NFE exome

AF:

0.151

Gnomad OTH exome

AF:

0.163

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00583

AC:

2330

AN:

399700

Hom.:

Cov.:

AF XY:

0.00594

AC XY:

1239

AN XY:

208416

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000252

AC:

AN:

11888

American (AMR)

AF:

0.0115

AC:

195

AN:

16918

Ashkenazi Jewish (ASJ)

AF:

0.00154

AC:

AN:

12350

East Asian (EAS)

AF:

0.0120

AC:

356

AN:

29626

South Asian (SAS)

AF:

0.0118

AC:

354

AN:

29878

European-Finnish (FIN)

AF:

0.00434

AC:

129

AN:

29712

Middle Eastern (MID)

AF:

0.00164

AC:

AN:

1830

European-Non Finnish (NFE)

AF:

0.00480

AC:

1169

AN:

243750

Other (OTH)

AF:

0.00430

AC:

102

AN:

23748

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.259

Heterozygous variant carriers

282

564

846

1128

1410

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000441

AC:

AN:

122338

Hom.:

Cov.:

AF XY:

0.000534

AC XY:

AN XY:

58046

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0000606

AC:

AN:

33020

American (AMR)

AF:

0.000360

AC:

AN:

11098

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3106

East Asian (EAS)

AF:

0.00347

AC:

AN:

3748

South Asian (SAS)

AF:

0.000635

AC:

AN:

3148

European-Finnish (FIN)

AF:

0.000389

AC:

AN:

7714

Middle Eastern (MID)

AF:

0.00

AC:

AN:

272

European-Non Finnish (NFE)

AF:

0.000501

AC:

AN:

57868

Other (OTH)

AF:

0.000643

AC:

AN:

1556

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.246

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0240

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

5.9

Mutation Taster

=8/192

disease causing (fs/PTC)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over