rs1562902

Variant names:

• chr11-14896670-C-T
• rs1562902
• NM_001429699.1:c.2887-2286C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001429699.1(PDE3B):​c.2887-2286C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,944 control chromosomes in the GnomAD database, including 23,738 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 0.56 (23738 hom., cov: 31)
• Consequence: PDE3B NM_001429699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 39 publications found

Genes affected

PDE3B (HGNC:8779): (phosphodiesterase 3B) Enables 3',5'-cyclic-nucleotide phosphodiesterase activity. Involved in negative regulation of angiogenesis; negative regulation of cell adhesion; and negative regulation of lipid catabolic process. Located in membrane. Part of guanyl-nucleotide exchange factor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE3B	NM_001429699.1	c.2887-2286C>T		intron_variant	Intron 14 of 14		NP_001416628.1
PDE3B	NM_001429700.1	c.2887-2275C>T		intron_variant	Intron 14 of 14		NP_001416629.1
PDE3B	NR_190763.1	n.3417-2286C>T		intron_variant	Intron 16 of 16
PDE3B	NR_190764.1	n.3162-2286C>T		intron_variant	Intron 15 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84344 AN: 151826 Hom.: 23714 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.556 AC: 84425 AN: 151944 Hom.: 23738 Cov.: 31 AF XY: 0.560 AC XY: 41615 AN XY: 74248

African (AFR) AF: 0.512 AC: 21229 AN: 41438

American (AMR) AF: 0.612 AC: 9344 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2362 AN: 3468

East Asian (EAS) AF: 0.603 AC: 3120 AN: 5170

South Asian (SAS) AF: 0.589 AC: 2839 AN: 4822

European-Finnish (FIN) AF: 0.532 AC: 5599 AN: 10528

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38129 AN: 67936

Other (OTH) AF: 0.540 AC: 1136 AN: 2104

Alfa AF: 0.561 Hom.: 64109

Bravo AF: 0.556

Asia WGS AF: 0.552 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.42
PhyloP100		-1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1562902; hg19: chr11-14918216;