1-149003009-G-T

Variant names:

• chr1-149003009-G-T
• rs147815016
• NM_001395426.1:c.3931G>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_001395426.1(PDE4DIP):​c.3931G>T​(p.Ala1311Ser) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1311T) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 20)
  • Exomes 𝑓: 0.0000071 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PDE4DIP NM_001395426.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.46
• Publications: 9 publications found

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

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.30979317).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE4DIP	NM_001395426.1	MANE Select	c.3931G>T	p.Ala1311Ser	missense	Exon 28 of 47	NP_001382355.1	A0A8Q3SI83
	PDE4DIP	NM_001395297.1		c.4222G>T	p.Ala1408Ser	missense	Exon 21 of 40	NP_001382226.1
	PDE4DIP	NM_001350520.2		c.4222G>T	p.Ala1408Ser	missense	Exon 21 of 40	NP_001337449.1	A0A994J5E0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE4DIP	ENST00000695795.1	MANE Select	c.3931G>T	p.Ala1311Ser	missense	Exon 28 of 47	ENSP00000512175.1	A0A8Q3SI83
	PDE4DIP	ENST00000369356.8	TSL:1	c.3733G>T	p.Ala1245Ser	missense	Exon 25 of 44	ENSP00000358363.4	Q5VU43-4
	PDE4DIP	ENST00000369354.7	TSL:1	c.3733G>T	p.Ala1245Ser	missense	Exon 25 of 44	ENSP00000358360.3	Q5VU43-1

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD2 exomes AF: 0.00000797 AC: 2 AN: 250922 AF XY: 0.0000148

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000882

Gnomad OTH exome AF: 0.000163

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000711 AC: 4 AN: 562914 Hom.: 0 Cov.: 6 AF XY: 0.0000133 AC XY: 4 AN XY: 300504

African (AFR) AF: 0.00 AC: 0 AN: 14906

American (AMR) AF: 0.00 AC: 0 AN: 27914

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14698

East Asian (EAS) AF: 0.00 AC: 0 AN: 35418

South Asian (SAS) AF: 0.0000188 AC: 1 AN: 53136

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49286

Middle Eastern (MID) AF: 0.000462 AC: 1 AN: 2164

European-Non Finnish (NFE) AF: 0.00000298 AC: 1 AN: 335618

Other (OTH) AF: 0.0000336 AC: 1 AN: 29774

GnomAD4 genome Cov.: 20

EpiCase AF: 0.00689

EpiControl AF: 0.00738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_noAF	Pathogenic	0.22
CADD	Uncertain	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.035	T
LIST_S2	Uncertain	0.89	D
MetaRNN	Benign	0.31	T
PhyloP100		5.5
PROVEAN	Benign	-1.5	N
Sift	Uncertain	0.014	D
Sift4G	Benign	0.10	T
Vest4		0.58
gMVP		0.47

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

Other links and lift over

dbSNP: rs147815016; hg19: chr1-144881463;