rs11023332

chr11-14762564-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000922.4(PDE3B):c.979-9373G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,964 control chromosomes in the GnomAD database, including 11,203 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 0.36 (11203 hom., cov: 32)
• Consequence: PDE3B NM_000922.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE3B	NM_000922.4	c.979-9373G>C		intron_variant		ENST00000282096.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE3B	ENST00000282096.9	c.979-9373G>C		intron_variant		1	NM_000922.4	P2
PDE3B	ENST00000455098.2	c.979-9373G>C		intron_variant		1		A2
PDE3B	ENST00000534317.1	n.795-9373G>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54436 AN: 151844 Hom.: 11204 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.358 AC: 54448 AN: 151964 Hom.: 11203 Cov.: 32 AF XY: 0.365 AC XY: 27091 AN XY: 74244

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.367

Alfa AF: 0.418 Hom.: 7594

Bravo AF: 0.349

Asia WGS AF: 0.375 AC: 1306 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	8.2
Dann	Benign	0.80

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

Other links and lift over

dbSNP: rs11023332; hg19: chr11-14784110;