1-148962619-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 1P and 3B. PP3 BP6_Moderate BP7

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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.37

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 Likely_benign. Variant got -2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE4DIP	NM_001395426.1	c.1371G>A	p.Glu457=	synonymous_variant	12/47	ENST00000695795.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE4DIP	ENST00000695795.1	c.1371G>A	p.Glu457=	synonymous_variant	12/47		NM_001395426.1

Frequencies

GnomAD3 genomes AF: 0.000245 AC: 31 AN: 126516 Hom.: 0 Cov.: 16

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: 54 AN: 251412 Hom.: 0 AF XY: 0.000213 AC XY: 29 AN XY: 135880

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.: 2 Cov.: 4 AF XY: 0.000462 AC XY: 111 AN XY: 240022

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: 31 AN: 126622 Hom.: 0 Cov.: 16 AF XY: 0.000334 AC XY: 20 AN XY: 59926

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.: 0

Bravo AF: 0.000276

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

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

Other links and lift over

dbSNP: rs201567215; hg19: chr1-144921856; COSMIC: COSV57684515;