Variant 1-148962619-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP3BP6_ModerateBP7BS2

The NM_001395426.1(PDE4DIP):c.1371G>A(p.Glu457=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00024 ( 0 hom., cov: 16)

Exomes 𝑓: 0.00045 ( 2 hom. )

Consequence

PDE4DIP
NM_001395426.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.37

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 Likely_benign. Variant got -6 ACMG points.

PP3

BayesDel_noAF computational evidence supports a deleterious effect, 0.15

BP6

Variant 1-148962619-G-A is Benign according to our data. Variant chr1-148962619-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2639073.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.37 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE4DIP	NM_001395426.1 linkuse as main transcript	c.1371G>A	p.Glu457=	synonymous_variant	12/47	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.1371G>A	p.Glu457=	synonymous_variant	12/47		NM_001395426.1	ENSP00000512175

Frequencies

GnomAD3 genomes

AF:

0.000245

AC:

AN:

126516

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000310

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000835

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00569

Gnomad SAS

AF:

0.000613

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000165

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000215

AC:

AN:

251412

Hom.:

AF XY:

0.000213

AC XY:

AN XY:

135880

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00213

Gnomad SAS exome

AF:

0.000425

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000326

GnomAD4 exome

AF:

0.000450

AC:

205

AN:

455602

Hom.:

Cov.:

AF XY:

0.000462

AC XY:

111

AN XY:

240022

show subpopulations

Gnomad4 AFR exome

AF:

0.0000775

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00524

Gnomad4 SAS exome

AF:

0.000664

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000735

Gnomad4 OTH exome

AF:

0.000114

GnomAD4 genome

AF:

0.000245

AC:

AN:

126622

Hom.:

Cov.:

AF XY:

0.000334

AC XY:

AN XY:

59926

show subpopulations

Gnomad4 AFR

AF:

0.0000309

Gnomad4 AMR

AF:

0.0000834

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00570

Gnomad4 SAS

AF:

0.000614

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000165

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000169

Hom.:

Bravo

AF:

0.000276

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

Mar 01, 2023

PDE4DIP: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Pathogenic

0.15

CADD

Benign

8.1

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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