11-72587236-C-T

Position:

• chr11-72587236-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002599.5(PDE2A):​c.1071-1055G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,194 control chromosomes in the GnomAD database, including 1,449 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 0.14 (1449 hom., cov: 32)
• Consequence: PDE2A NM_002599.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

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]

PDE2A-AS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE2A	NM_002599.5	c.1071-1055G>A		intron_variant		ENST00000334456.10	NP_002590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE2A	ENST00000334456.10	c.1071-1055G>A		intron_variant		1	NM_002599.5	ENSP00000334910.5

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20774 AN: 152074 Hom.: 1446 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0723

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.137 AC: 20795 AN: 152194 Hom.: 1449 Cov.: 32 AF XY: 0.137 AC XY: 10193 AN XY: 74406

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0722

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.115

Alfa AF: 0.129 Hom.: 1735

Bravo AF: 0.136

Asia WGS AF: 0.0960 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.43

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

Other links and lift over

dbSNP: rs341048; hg19: chr11-72298280;