1-148893214-A-T

Position:

• chr1-148893214-A-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2 BP4_Strong BS1

The NM_001395426.1(PDE4DIP):​c.339+3320A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00388 in 120,324 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0039 (0 hom., cov: 21)
• Consequence: PDE4DIP NM_001395426.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00388 (467/120324) while in subpopulation EAS AF= 0.0306 (89/2908). AF 95% confidence interval is 0.0255. There are 0 homozygotes in gnomad4. There are 250 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE4DIP	NM_001395426.1	c.339+3320A>T		intron_variant		ENST00000695795.1	NP_001382355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE4DIP	ENST00000695795.1	c.339+3320A>T		intron_variant			NM_001395426.1	ENSP00000512175.1

Frequencies

GnomAD3 genomes AF: 0.00384 AC: 462 AN: 120282 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.00371

Gnomad AMI AF: 0.00259

Gnomad AMR AF: 0.00672

Gnomad ASJ AF: 0.00272

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.00223

Gnomad FIN AF: 0.00324

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00226

Gnomad OTH AF: 0.00311

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00388 AC: 467 AN: 120324 Hom.: 0 Cov.: 21 AF XY: 0.00431 AC XY: 250 AN XY: 58066

Gnomad4 AFR AF: 0.00376

Gnomad4 AMR AF: 0.00672

Gnomad4 ASJ AF: 0.00272

Gnomad4 EAS AF: 0.0306

Gnomad4 SAS AF: 0.00251

Gnomad4 FIN AF: 0.00324

Gnomad4 NFE AF: 0.00226

Gnomad4 OTH AF: 0.00432

Alfa AF: 0.110 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.67

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: rs1778596; hg19: chr1-144991278;