11-14893764-A-G

Variant names:

• chr11-14893764-A-G
• rs2060793
• NM_001429699.1:c.2887-5192A>G

Variant summary

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

The NM_001429699.1(PDE3B):​c.2887-5192A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 151,972 control chromosomes in the GnomAD database, including 30,253 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 0.63 (30253 hom., cov: 31)
• Consequence: PDE3B NM_001429699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 129 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 = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001429699.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE3B	NM_001429699.1		c.2887-5192A>G		intron	N/A	NP_001416628.1
	PDE3B	NM_001429700.1		c.2887-5181A>G		intron	N/A	NP_001416629.1
	PDE3B	NR_190763.1		n.3416+4458A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95441 AN: 151854 Hom.: 30208 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.629 AC: 95550 AN: 151972 Hom.: 30253 Cov.: 31 AF XY: 0.634 AC XY: 47061 AN XY: 74268

African (AFR) AF: 0.645 AC: 26713 AN: 41424

American (AMR) AF: 0.666 AC: 10172 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2516 AN: 3472

East Asian (EAS) AF: 0.658 AC: 3397 AN: 5166

South Asian (SAS) AF: 0.660 AC: 3183 AN: 4820

European-Finnish (FIN) AF: 0.578 AC: 6094 AN: 10540

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41344 AN: 67972

Other (OTH) AF: 0.619 AC: 1306 AN: 2110

Alfa AF: 0.620 Hom.: 119728

Bravo AF: 0.635

Asia WGS AF: 0.638 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs2060793; hg19: chr11-14915310;