11-72612844-G-T

Variant summary

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

The NM_002599.5(PDE2A):​c.145-4093C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,122 control chromosomes in the GnomAD database, including 52,478 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 0.83 ( 52478 hom., cov: 31)

Consequence

PDE2A
NM_002599.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.754
Variant links:
Genes affected
PDE2A (HGNC:8777): (phosphodiesterase 2A) Enables several functions, including 3',5'-cyclic-nucleotide phosphodiesterase activity; anion binding activity; and metal ion binding activity. Involved in several processes, including cellular response to organic cyclic compound; cyclic-nucleotide-mediated signaling; and regulation of vascular permeability. Located in several cellular components, including cytosol; mitochondrial membrane; and perinuclear region of cytoplasm. Colocalizes with plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PDE2ANM_002599.5 linkc.145-4093C>A intron_variant Intron 2 of 30 ENST00000334456.10 NP_002590.1 O00408-1Q8IW54

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PDE2AENST00000334456.10 linkc.145-4093C>A intron_variant Intron 2 of 30 1 NM_002599.5 ENSP00000334910.5 O00408-1

Frequencies

GnomAD3 genomes
AF:
0.829
AC:
126033
AN:
152004
Hom.:
52423
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.881
Gnomad AMI
AF:
0.846
Gnomad AMR
AF:
0.831
Gnomad ASJ
AF:
0.769
Gnomad EAS
AF:
0.925
Gnomad SAS
AF:
0.868
Gnomad FIN
AF:
0.792
Gnomad MID
AF:
0.867
Gnomad NFE
AF:
0.795
Gnomad OTH
AF:
0.839
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.829
AC:
126141
AN:
152122
Hom.:
52478
Cov.:
31
AF XY:
0.829
AC XY:
61674
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.881
Gnomad4 AMR
AF:
0.831
Gnomad4 ASJ
AF:
0.769
Gnomad4 EAS
AF:
0.925
Gnomad4 SAS
AF:
0.868
Gnomad4 FIN
AF:
0.792
Gnomad4 NFE
AF:
0.795
Gnomad4 OTH
AF:
0.840
Alfa
AF:
0.812
Hom.:
6231
Bravo
AF:
0.833
Asia WGS
AF:
0.895
AC:
3113
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
0.65

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: rs907849; hg19: chr11-72323888; API