rs918590

Variant summary

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

The ENST00000502484.6(PDE4D):​c.-90+85961T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,072 control chromosomes in the GnomAD database, including 8,695 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 0.32 ( 8695 hom., cov: 32)

Consequence

PDE4D
ENST00000502484.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.104
Variant links:
Genes affected
PDE4D (HGNC:8783): (phosphodiesterase 4D) This gene encodes one of four mammalian counterparts to the fruit fly 'dunce' gene. The encoded protein has 3',5'-cyclic-AMP phosphodiesterase activity and degrades cAMP, which acts as a signal transduction molecule in multiple cell types. This gene uses different promoters to generate multiple alternatively spliced transcript variants that encode functional proteins.[provided by RefSeq, Sep 2009]

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=-0.66).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PDE4DNM_001165899.2 linkuse as main transcriptc.-90+85961T>G intron_variant NP_001159371.1
PDE4DNM_001349241.2 linkuse as main transcriptc.-193+85961T>G intron_variant NP_001336170.1
PDE4DNM_001349243.2 linkuse as main transcriptc.-674+85961T>G intron_variant NP_001336172.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PDE4DENST00000502484.6 linkuse as main transcriptc.-90+85961T>G intron_variant 1 ENSP00000423094 Q08499-11
PDE4DENST00000509355.5 linkuse as main transcriptn.157+85961T>G intron_variant, non_coding_transcript_variant 1
PDE4DENST00000505507.6 linkuse as main transcriptc.-213+85961T>G intron_variant 4 ENSP00000425910

Frequencies

GnomAD3 genomes
AF:
0.316
AC:
47956
AN:
151954
Hom.:
8678
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.472
Gnomad AMI
AF:
0.252
Gnomad AMR
AF:
0.280
Gnomad ASJ
AF:
0.207
Gnomad EAS
AF:
0.532
Gnomad SAS
AF:
0.494
Gnomad FIN
AF:
0.170
Gnomad MID
AF:
0.291
Gnomad NFE
AF:
0.229
Gnomad OTH
AF:
0.292
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.316
AC:
47999
AN:
152072
Hom.:
8695
Cov.:
32
AF XY:
0.316
AC XY:
23456
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.472
Gnomad4 AMR
AF:
0.279
Gnomad4 ASJ
AF:
0.207
Gnomad4 EAS
AF:
0.531
Gnomad4 SAS
AF:
0.493
Gnomad4 FIN
AF:
0.170
Gnomad4 NFE
AF:
0.229
Gnomad4 OTH
AF:
0.300
Alfa
AF:
0.236
Hom.:
4283
Bravo
AF:
0.327
Asia WGS
AF:
0.531
AC:
1846
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
11
DANN
Benign
0.81

Splicing

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: rs918590; hg19: chr5-59697808; API