rs546784

chr1-66296783-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002600.4(PDE4B):c.634+30696T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,056 control chromosomes in the GnomAD database, including 15,706 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 0.42 (15706 hom., cov: 32)
• Consequence: PDE4B NM_002600.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE4B	NM_002600.4	c.634+30696T>C		intron_variant		ENST00000341517.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE4B	ENST00000341517.9	c.634+30696T>C		intron_variant		1	NM_002600.4	A1
PDE4B	ENST00000329654.8	c.634+30696T>C		intron_variant		1		A1
PDE4B	ENST00000423207.6	c.589+30696T>C		intron_variant		1		P3
PDE4B	ENST00000412480.6	c.358+30696T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63697 AN: 151938 Hom.: 15706 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.419 AC: 63701 AN: 152056 Hom.: 15706 Cov.: 32 AF XY: 0.417 AC XY: 31009 AN XY: 74318

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.398

Alfa AF: 0.517 Hom.: 13000

Bravo AF: 0.390

Asia WGS AF: 0.230 AC: 800 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	4.9
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: rs546784; hg19: chr1-66762466;