rs12124527

Variant names:

• chr1-148988155-G-A
• rs12124527
• NM_001395426.1:c.3014-3730G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-148988155-G-A
• chr1-148988155-G-C
• chr1-148988155-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395426.1(PDE4DIP):​c.3014-3730G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,932 control chromosomes in the GnomAD database, including 31,685 homozygotes. 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 0.63 (31685 hom., cov: 31)
• Consequence: PDE4DIP NM_001395426.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 13 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE4DIP	NM_001395426.1	c.3014-3730G>A		intron_variant	Intron 24 of 46	ENST00000695795.1	NP_001382355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE4DIP	ENST00000695795.1	c.3014-3730G>A		intron_variant	Intron 24 of 46		NM_001395426.1	ENSP00000512175.1

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96220 AN: 151812 Hom.: 31634 Cov.: 31

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.634 AC: 96332 AN: 151932 Hom.: 31685 Cov.: 31 AF XY: 0.636 AC XY: 47190 AN XY: 74232

African (AFR) AF: 0.831 AC: 34462 AN: 41454

American (AMR) AF: 0.568 AC: 8667 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2114 AN: 3468

East Asian (EAS) AF: 0.597 AC: 3085 AN: 5168

South Asian (SAS) AF: 0.606 AC: 2923 AN: 4822

European-Finnish (FIN) AF: 0.561 AC: 5914 AN: 10544

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37215 AN: 67906

Other (OTH) AF: 0.605 AC: 1277 AN: 2110

Alfa AF: 0.577 Hom.: 50148

Bravo AF: 0.640

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.067
PhyloP100		-1.1

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: rs12124527; hg19: chr1-144896319;