rs536025

Variant names:

• chr1-66166947-G-A
• rs536025
• NM_002600.4:c.282-80513G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-66166947-G-A
• chr1-66166947-G-C
• chr1-66166947-G-T

Variant summary

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

The NM_002600.4(PDE4B):​c.282-80513G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,130 control chromosomes in the GnomAD database, including 43,338 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 0.75 (43338 hom., cov: 32)
• Consequence: PDE4B NM_002600.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 1 publications found

Genes affected

PDE4B (HGNC:8781): (phosphodiesterase 4B) This gene is a member of the type IV, cyclic AMP (cAMP)-specific, cyclic nucleotide phosphodiesterase (PDE) family. The encoded protein regulates the cellular concentrations of cyclic nucleotides and thereby play a role in signal transduction. Altered activity of this protein has been associated with schizophrenia and bipolar affective disorder. Alternative splicing and the use of alternative promoters results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE4B	NM_002600.4	c.282-80513G>A		intron_variant	Intron 3 of 16	ENST00000341517.9	NP_002591.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE4B	ENST00000341517.9	c.282-80513G>A		intron_variant	Intron 3 of 16	1	NM_002600.4	ENSP00000342637.4

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114116 AN: 152012 Hom.: 43276 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.751 AC: 114237 AN: 152130 Hom.: 43338 Cov.: 32 AF XY: 0.754 AC XY: 56102 AN XY: 74364

African (AFR) AF: 0.857 AC: 35573 AN: 41512

American (AMR) AF: 0.705 AC: 10785 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2376 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4603 AN: 5192

South Asian (SAS) AF: 0.792 AC: 3812 AN: 4814

European-Finnish (FIN) AF: 0.749 AC: 7913 AN: 10558

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46780 AN: 67974

Other (OTH) AF: 0.738 AC: 1558 AN: 2112

Alfa AF: 0.734 Hom.: 7189

Bravo AF: 0.751

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.34
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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: rs536025; hg19: chr1-66632630;