11-72577606-TG-T

Position:

• chr11-72577606-TG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002599.5(PDE2A):​c.2616-13del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.60 (28229 hom., cov: 0)
  • Exomes 𝑓: 0.51 (190182 hom.)
• Consequence: PDE2A NM_002599.5 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.297

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-72577606-TG-T is Benign according to our data. Variant chr11-72577606-TG-T is described in ClinVar as [Benign]. Clinvar id is 1168226.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE2A	NM_002599.5	c.2616-13del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000334456.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE2A	ENST00000334456.10	c.2616-13del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_002599.5	A1

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90414 AN: 151556 Hom.: 28188 Cov.: 0

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.550

GnomAD3 exomes AF: 0.576 AC: 137126 AN: 238258 Hom.: 41554 AF XY: 0.559 AC XY: 72448 AN XY: 129582

Gnomad AFR exome AF: 0.780

Gnomad AMR exome AF: 0.741

Gnomad ASJ exome AF: 0.525

Gnomad EAS exome AF: 0.746

Gnomad SAS exome AF: 0.577

Gnomad FIN exome AF: 0.593

Gnomad NFE exome AF: 0.471

Gnomad OTH exome AF: 0.537

GnomAD4 exome AF: 0.508 AC: 724522 AN: 1427364 Hom.: 190182 Cov.: 0 AF XY: 0.508 AC XY: 361392 AN XY: 711608

Gnomad4 AFR exome AF: 0.782

Gnomad4 AMR exome AF: 0.728

Gnomad4 ASJ exome AF: 0.522

Gnomad4 EAS exome AF: 0.760

Gnomad4 SAS exome AF: 0.577

Gnomad4 FIN exome AF: 0.598

Gnomad4 NFE exome AF: 0.471

Gnomad4 OTH exome AF: 0.524

GnomAD4 genome AF: 0.597 AC: 90509 AN: 151674 Hom.: 28229 Cov.: 0 AF XY: 0.603 AC XY: 44722 AN XY: 74124

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.552

Alfa AF: 0.228 Hom.: 235

Bravo AF: 0.605

Asia WGS AF: 0.661 AC: 2297 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3842266; hg19: chr11-72288650;