Variant chr1-148953512-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000313431.13(PDE4DIP):c.732T>G(p.Ser244=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00366 in 1,613,870 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0030 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0037 ( 9 hom. )

Consequence

PDE4DIP
ENST00000313431.13 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.103

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 1-148953512-T-G is Benign according to our data. Variant chr1-148953512-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2639078.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.103 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE4DIP	NM_001395426.1 linkuse as main transcript	c.835-7142T>G		intron_variant		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.835-7142T>G		intron_variant			NM_001395426.1	ENSP00000512175

Frequencies

GnomAD3 genomes

AF:

0.00300

AC:

456

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000362

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00406

Gnomad ASJ

AF:

0.0170

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00703

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00395

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00379

AC:

952

AN:

251186

Hom.:

AF XY:

0.00436

AC XY:

592

AN XY:

135742

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.00214

Gnomad ASJ exome

AF:

0.0150

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00641

Gnomad FIN exome

AF:

0.000370

Gnomad NFE exome

AF:

0.00431

Gnomad OTH exome

AF:

0.00489

GnomAD4 exome

AF:

0.00373

AC:

5451

AN:

1461542

Hom.:

Cov.:

AF XY:

0.00400

AC XY:

2909

AN XY:

727098

show subpopulations

Gnomad4 AFR exome

AF:

0.000359

Gnomad4 AMR exome

AF:

0.00282

Gnomad4 ASJ exome

AF:

0.0165

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00729

Gnomad4 FIN exome

AF:

0.000300

Gnomad4 NFE exome

AF:

0.00348

Gnomad4 OTH exome

AF:

0.00477

GnomAD4 genome

AF:

0.00299

AC:

456

AN:

152328

Hom.:

Cov.:

AF XY:

0.00290

AC XY:

216

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.000361

Gnomad4 AMR

AF:

0.00405

Gnomad4 ASJ

AF:

0.0170

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00704

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00395

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00345

Hom.:

Bravo

AF:

0.00321

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

Apr 01, 2023

PDE4DIP: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.57

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