rs11576970

Positions:

• chr1-66121129-C-T

Variant summary

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

The NM_002600.4(PDE4B):​c.282-126331C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0622 in 152,136 control chromosomes in the GnomAD database, including 436 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 0.062 (436 hom., cov: 32)
• Consequence: PDE4B NM_002600.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE4B	NM_002600.4	c.282-126331C>T		intron_variant		ENST00000341517.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE4B	ENST00000341517.9	c.282-126331C>T		intron_variant		1	NM_002600.4	A1

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9444 AN: 152018 Hom.: 434 Cov.: 32

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0817

Gnomad OTH AF: 0.0881

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

GnomAD4 genome AF: 0.0622 AC: 9466 AN: 152136 Hom.: 436 Cov.: 32 AF XY: 0.0615 AC XY: 4577 AN XY: 74364

Gnomad4 AFR AF: 0.0180

Gnomad4 AMR AF: 0.0775

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0342

Gnomad4 NFE AF: 0.0817

Gnomad4 OTH AF: 0.0905

Alfa AF: 0.0664 Hom.: 48

Bravo AF: 0.0614

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.40

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: rs11576970; hg19: chr1-66586812; COSMIC: COSV58471191;