rs2910830

Variant summary

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

The ENST00000502484.6(PDE4D):​c.42+14181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,768 control chromosomes in the GnomAD database, including 27,842 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 0.60 ( 27842 hom., cov: 32)

Consequence

PDE4D
ENST00000502484.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15
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=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PDE4DNM_001165899.2 linkuse as main transcriptc.42+14181C>T intron_variant
PDE4DNM_001349241.2 linkuse as main transcriptc.-62+14181C>T intron_variant
PDE4DNM_001349243.2 linkuse as main transcriptc.-543+14181C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PDE4DENST00000502484.6 linkuse as main transcriptc.42+14181C>T intron_variant 1 Q08499-11
PDE4DENST00000509368.6 linkuse as main transcriptc.43-10559C>T intron_variant, NMD_transcript_variant 1
PDE4DENST00000509355.5 linkuse as main transcriptn.288+14181C>T intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.601
AC:
91076
AN:
151650
Hom.:
27828
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.556
Gnomad AMI
AF:
0.774
Gnomad AMR
AF:
0.636
Gnomad ASJ
AF:
0.635
Gnomad EAS
AF:
0.240
Gnomad SAS
AF:
0.599
Gnomad FIN
AF:
0.654
Gnomad MID
AF:
0.614
Gnomad NFE
AF:
0.635
Gnomad OTH
AF:
0.598
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.600
AC:
91118
AN:
151768
Hom.:
27842
Cov.:
32
AF XY:
0.598
AC XY:
44333
AN XY:
74146
show subpopulations
Gnomad4 AFR
AF:
0.556
Gnomad4 AMR
AF:
0.637
Gnomad4 ASJ
AF:
0.635
Gnomad4 EAS
AF:
0.239
Gnomad4 SAS
AF:
0.599
Gnomad4 FIN
AF:
0.654
Gnomad4 NFE
AF:
0.635
Gnomad4 OTH
AF:
0.592
Alfa
AF:
0.627
Hom.:
60854
Bravo
AF:
0.597
Asia WGS
AF:
0.411
AC:
1431
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.31
DANN
Benign
0.67

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: rs2910830; hg19: chr5-59467203; API