1-148953512-T-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.103

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]

ACMG classification

Verdict is Benign. Variant got -7 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE4DIP	NM_001395426.1	c.835-7142T>G		intron_variant		ENST00000695795.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE4DIP	ENST00000695795.1	c.835-7142T>G		intron_variant			NM_001395426.1

Frequencies

GnomAD3 genomes AF: 0.00300 AC: 456 AN: 152210 Hom.: 0 Cov.: 31

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.: 0 AF XY: 0.00436 AC XY: 592 AN XY: 135742

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.: 9 Cov.: 32 AF XY: 0.00400 AC XY: 2909 AN XY: 727098

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.: 0 Cov.: 31 AF XY: 0.00290 AC XY: 216 AN XY: 74488

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.: 0

Bravo AF: 0.00321

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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	15
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

Other links and lift over

dbSNP: rs143410813; hg19: chr1-144930977;