1-148962551-C-G

Variant names:

• chr1-148962551-C-G
• rs71664015
• NM_001395426.1:c.1303C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001395426.1(PDE4DIP):​c.1303C>G​(p.Leu435Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L435L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 16)
• Consequence: PDE4DIP NM_001395426.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

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.

• BP4: Computational evidence support a benign effect (MetaRNN=0.23848435).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE4DIP	NM_001395426.1	c.1303C>G	p.Leu435Val	missense_variant	Exon 12 of 47	ENST00000695795.1	NP_001382355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE4DIP	ENST00000695795.1	c.1303C>G	p.Leu435Val	missense_variant	Exon 12 of 47		NM_001395426.1	ENSP00000512175.1

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Cov.: 5

GnomAD4 genome Cov.: 16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_noAF	Pathogenic	0.16
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.080	.;T;.;T;.;T;.;.;.;.;.
LIST_S2	Benign	0.85	D;D;D;T;D;D;D;D;D;D;D
MetaRNN	Benign	0.24	T;T;T;T;T;T;T;T;T;T;T
PROVEAN	Benign	-1.7	.;.;.;.;N;N;N;N;N;N;N
Sift	Uncertain	0.028	.;.;.;.;D;D;T;D;D;T;T
Sift4G	Benign	0.14	T;T;T;T;T;T;T;T;T;T;T
Vest4		0.39
gMVP		0.88

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: rs71664015; hg19: chr1-144921924;