rs10493399

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002600.4(PDE4B):​c.282-38140T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0127 in 152,350 control chromosomes in the GnomAD database, including 91 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 0.013 ( 91 hom., cov: 32)

Consequence

PDE4B
NM_002600.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.592
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PDE4BNM_002600.4 linkuse as main transcriptc.282-38140T>C intron_variant ENST00000341517.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PDE4BENST00000341517.9 linkuse as main transcriptc.282-38140T>C intron_variant 1 NM_002600.4 A1Q07343-1

Frequencies

GnomAD3 genomes
AF:
0.0127
AC:
1936
AN:
152232
Hom.:
88
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00217
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00785
Gnomad ASJ
AF:
0.00461
Gnomad EAS
AF:
0.147
Gnomad SAS
AF:
0.0679
Gnomad FIN
AF:
0.0106
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00703
Gnomad OTH
AF:
0.0115
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0127
AC:
1941
AN:
152350
Hom.:
91
Cov.:
32
AF XY:
0.0149
AC XY:
1112
AN XY:
74496
show subpopulations
Gnomad4 AFR
AF:
0.00216
Gnomad4 AMR
AF:
0.00784
Gnomad4 ASJ
AF:
0.00461
Gnomad4 EAS
AF:
0.147
Gnomad4 SAS
AF:
0.0676
Gnomad4 FIN
AF:
0.0106
Gnomad4 NFE
AF:
0.00703
Gnomad4 OTH
AF:
0.0161
Alfa
AF:
0.0131
Hom.:
7
Bravo
AF:
0.0110
Asia WGS
AF:
0.0950
AC:
330
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
8.4
DANN
Benign
0.58

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10493399; hg19: chr1-66675003; API