Variant chr1-149003009-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_001395426.1(PDE4DIP):c.3931G>A(p.Ala1311Thr) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 3 hom., cov: 20)

Exomes 𝑓: 0.0049 ( 12 hom. )

Failed GnomAD Quality Control

Consequence

PDE4DIP
NM_001395426.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.46

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 made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.08840865).

BP6

Variant 1-149003009-G-A is Benign according to our data. Variant chr1-149003009-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3024762.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE4DIP	NM_001395426.1 linkuse as main transcript	c.3931G>A	p.Ala1311Thr	missense_variant	28/47	ENST00000695795.1	NP_001382355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE4DIP	ENST00000695795.1 linkuse as main transcript	c.3931G>A	p.Ala1311Thr	missense_variant	28/47		NM_001395426.1	ENSP00000512175

Frequencies

GnomAD3 genomes

AF:

0.00468

AC:

701

AN:

149942

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00180

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00870

Gnomad ASJ

AF:

0.00204

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000214

Gnomad FIN

AF:

0.000480

Gnomad MID

AF:

0.00641

Gnomad NFE

AF:

0.00682

Gnomad OTH

AF:

0.0112

GnomAD3 exomes

AF:

0.00342

AC:

858

AN:

250922

Hom.:

AF XY:

0.00354

AC XY:

480

AN XY:

135578

show subpopulations

Gnomad AFR exome

AF:

0.000924

Gnomad AMR exome

AF:

0.00533

Gnomad ASJ exome

AF:

0.00298

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.000277

Gnomad NFE exome

AF:

0.00526

Gnomad OTH exome

AF:

0.00376

GnomAD4 exome

AF:

0.00488

AC:

2749

AN:

562878

Hom.:

Cov.:

AF XY:

0.00479

AC XY:

1439

AN XY:

300482

show subpopulations

Gnomad4 AFR exome

AF:

0.00148

Gnomad4 AMR exome

AF:

0.00763

Gnomad4 ASJ exome

AF:

0.00320

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000376

Gnomad4 FIN exome

AF:

0.000528

Gnomad4 NFE exome

AF:

0.00664

Gnomad4 OTH exome

AF:

0.00611

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00466

AC:

699

AN:

150054

Hom.:

Cov.:

AF XY:

0.00395

AC XY:

289

AN XY:

73144

show subpopulations

Gnomad4 AFR

AF:

0.00179

Gnomad4 AMR

AF:

0.00869

Gnomad4 ASJ

AF:

0.00204

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000214

Gnomad4 FIN

AF:

0.000480

Gnomad4 NFE

AF:

0.00682

Gnomad4 OTH

AF:

0.0111

Alfa

AF:

0.00610

Hom.:

Bravo

AF:

0.00569

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

PDE4DIP: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_noAF

Pathogenic

0.33

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.070

.;T;.;.;T

LIST_S2

Uncertain

0.91

D;D;T;D;D

MetaRNN

Benign

0.088

T;T;T;T;T

PROVEAN

Benign

-2.1

.;.;.;N;N

Sift

Benign

0.064

.;.;.;T;T

Sift4G

Benign

0.13

T;T;T;T;T

Vest4

0.59

gMVP

0.58

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over