dbSNP rs151144469: PDE4DIP:p.His450His (chr1-148962598-C-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001395426.1(PDE4DIP):c.1350C>T(p.His450His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000063 ( 0 hom., cov: 16)

Exomes 𝑓: 0.000026 ( 0 hom. )

Consequence

PDE4DIP
NM_001395426.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.50

Publications

5 publications found

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 was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 1-148962598-C-T is Benign according to our data. Variant chr1-148962598-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2639074.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.5 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395426.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PDE4DIP	NM_001395426.1	MANE Select	c.1350C>T	p.His450His	synonymous	Exon 12 of 47	NP_001382355.1	A0A8Q3SI83
PDE4DIP	NM_001395297.1		c.1641C>T	p.His547His	synonymous	Exon 5 of 40	NP_001382226.1
PDE4DIP	NM_001350520.2		c.1641C>T	p.His547His	synonymous	Exon 5 of 40	NP_001337449.1	A0A994J5E0

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PDE4DIP	ENST00000695795.1	MANE Select	c.1350C>T	p.His450His	synonymous	Exon 12 of 47	ENSP00000512175.1	A0A8Q3SI83
PDE4DIP	ENST00000369356.8	TSL:1	c.1152C>T	p.His384His	synonymous	Exon 9 of 44	ENSP00000358363.4	Q5VU43-4
PDE4DIP	ENST00000369354.7	TSL:1	c.1152C>T	p.His384His	synonymous	Exon 9 of 44	ENSP00000358360.3	Q5VU43-1

Frequencies

GnomAD3 genomes

AF:

0.0000632

AC:

AN:

126632

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000126

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000115

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00522

AC:

1312

AN:

251140

AF XY:

0.00507

show subpopulations

Gnomad AFR exome

AF:

0.00142

Gnomad AMR exome

AF:

0.000868

Gnomad ASJ exome

AF:

0.000794

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00705

Gnomad NFE exome

AF:

0.00944

Gnomad OTH exome

AF:

0.00392

GnomAD4 exome

AF:

0.0000256

AC:

AN:

468424

Hom.:

Cov.:

AF XY:

0.0000202

AC XY:

AN XY:

247856

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

13286

American (AMR)

AF:

0.00

AC:

AN:

20118

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14116

East Asian (EAS)

AF:

0.0000918

AC:

AN:

32688

South Asian (SAS)

AF:

0.00

AC:

AN:

48346

European-Finnish (FIN)

AF:

0.0000634

AC:

AN:

31564

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2068

European-Non Finnish (NFE)

AF:

0.0000215

AC:

AN:

279506

Other (OTH)

AF:

0.0000374

AC:

AN:

26732

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000632

AC:

AN:

126632

Hom.:

Cov.:

AF XY:

0.0000669

AC XY:

AN XY:

59816

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

32246

American (AMR)

AF:

0.00

AC:

AN:

11992

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3132

East Asian (EAS)

AF:

0.00

AC:

AN:

4504

South Asian (SAS)

AF:

0.00

AC:

AN:

3254

European-Finnish (FIN)

AF:

0.000126

AC:

AN:

7930

Middle Eastern (MID)

AF:

0.00

AC:

AN:

300

European-Non Finnish (NFE)

AF:

0.000115

AC:

AN:

60820

Other (OTH)

AF:

0.00

AC:

AN:

1610

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00313

Hom.:

ClinVar

ClinVar submissions as Germline

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.51

(source)

DANN

Benign

0.77

PhyloP100

-2.5

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over