chr1-66153895-G-A

Variant names:

• chr1-66153895-G-A
• rs2503166
• NM_002600.4:c.282-93565G>A

Variant summary

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

The NM_002600.4(PDE4B):​c.282-93565G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,020 control chromosomes in the GnomAD database, including 34,996 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 0.68 (34996 hom., cov: 31)
• Consequence: PDE4B NM_002600.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE4B	NM_002600.4	c.282-93565G>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.282-93565G>A		intron_variant	Intron 3 of 16	1	NM_002600.4	ENSP00000342637.4

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102553 AN: 151902 Hom.: 34980 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.675 AC: 102626 AN: 152020 Hom.: 34996 Cov.: 31 AF XY: 0.670 AC XY: 49761 AN XY: 74308

African (AFR) AF: 0.689 AC: 28560 AN: 41444

American (AMR) AF: 0.691 AC: 10555 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2477 AN: 3468

East Asian (EAS) AF: 0.420 AC: 2172 AN: 5170

South Asian (SAS) AF: 0.534 AC: 2573 AN: 4816

European-Finnish (FIN) AF: 0.623 AC: 6584 AN: 10560

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47334 AN: 67974

Other (OTH) AF: 0.675 AC: 1426 AN: 2112

Alfa AF: 0.684 Hom.: 6057

Bravo AF: 0.681

Asia WGS AF: 0.463 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.43
PhyloP100		-0.26
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: rs2503166; hg19: chr1-66619578;