11-14893332-A-G

Variant names:

• chr11-14893332-A-G
• rs10741657
• NM_001429699.1:c.2887-5624A>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.2887-5624A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,108 control chromosomes in the GnomAD database, including 33,012 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 0.65 (33012 hom., cov: 33)
• Consequence: PDE3B NM_001429699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 396 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 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.2887-5624A>G		intron	N/A	NP_001416628.1
	PDE3B	NM_001429700.1		c.2887-5613A>G		intron	N/A	NP_001416629.1
	PDE3B	NR_190763.1		n.3416+4026A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99456 AN: 151990 Hom.: 32953 Cov.: 33

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.655 AC: 99581 AN: 152108 Hom.: 33012 Cov.: 33 AF XY: 0.658 AC XY: 48924 AN XY: 74358

African (AFR) AF: 0.734 AC: 30482 AN: 41508

American (AMR) AF: 0.675 AC: 10319 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2515 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3407 AN: 5180

South Asian (SAS) AF: 0.662 AC: 3186 AN: 4814

European-Finnish (FIN) AF: 0.579 AC: 6111 AN: 10562

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.609 AC: 41378 AN: 67978

Other (OTH) AF: 0.641 AC: 1353 AN: 2112

Alfa AF: 0.624 Hom.: 101106

Bravo AF: 0.664

Asia WGS AF: 0.644 AC: 2240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.28
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10741657; hg19: chr11-14914878;