Variant chr11-72577555-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002599.5(PDE2A):c.2655C>T(p.Tyr885Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,607,156 control chromosomes in the GnomAD database, including 75,410 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 6624 hom., cov: 33)

Exomes 𝑓: 0.31 ( 68786 hom. )

Consequence

PDE2A
NM_002599.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0130

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]

PDE2A links:

PDE2A (HGNC:):

PDE2A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 11-72577555-G-A is Benign according to our data. Variant chr11-72577555-G-A is described in ClinVar as [Benign]. Clinvar id is 1167963.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.013 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE2A	NM_002599.5 linkuse as main transcript	c.2655C>T	p.Tyr885Tyr	synonymous_variant	31/31	ENST00000334456.10	NP_002590.1	O00408-1Q8IW54

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE2A	ENST00000334456.10 linkuse as main transcript	c.2655C>T	p.Tyr885Tyr	synonymous_variant	31/31	1	NM_002599.5	ENSP00000334910.5		O00408-1

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44850

AN:

151942

Hom.:

6618

Cov.:

show subpopulations

Gnomad AFR

AF:

0.269

Gnomad AMI

AF:

0.258

Gnomad AMR

AF:

0.289

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.343

Gnomad FIN

AF:

0.325

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.291

GnomAD3 exomes

AF:

0.300

AC:

73795

AN:

245666

Hom.:

11283

AF XY:

0.305

AC XY:

40591

AN XY:

133204

show subpopulations

Gnomad AFR exome

AF:

0.266

Gnomad AMR exome

AF:

0.260

Gnomad ASJ exome

AF:

0.371

Gnomad EAS exome

AF:

0.263

Gnomad SAS exome

AF:

0.349

Gnomad FIN exome

AF:

0.327

Gnomad NFE exome

AF:

0.300

Gnomad OTH exome

AF:

0.314

GnomAD4 exome

AF:

0.306

AC:

444894

AN:

1455094

Hom.:

68786

Cov.:

AF XY:

0.308

AC XY:

222960

AN XY:

724118

show subpopulations

Gnomad4 AFR exome

AF:

0.273

Gnomad4 AMR exome

AF:

0.259

Gnomad4 ASJ exome

AF:

0.363

Gnomad4 EAS exome

AF:

0.249

Gnomad4 SAS exome

AF:

0.350

Gnomad4 FIN exome

AF:

0.324

Gnomad4 NFE exome

AF:

0.305

Gnomad4 OTH exome

AF:

0.306

GnomAD4 genome

AF:

0.295

AC:

44882

AN:

152062

Hom.:

6624

Cov.:

AF XY:

0.297

AC XY:

22106

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.269

Gnomad4 AMR

AF:

0.289

Gnomad4 ASJ

AF:

0.360

Gnomad4 EAS

AF:

0.257

Gnomad4 SAS

AF:

0.343

Gnomad4 FIN

AF:

0.325

Gnomad4 NFE

AF:

0.305

Gnomad4 OTH

AF:

0.291

Alfa

AF:

0.309

Hom.:

1612

Bravo

AF:

0.290

Asia WGS

AF:

0.291

AC:

1012

AN:

3476

EpiCase

AF:

0.299

EpiControl

AF:

0.300

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

3.2

DANN

Benign

0.89

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over