rs11023332

Variant names:

• chr11-14762564-G-C
• rs11023332
• NM_000922.4:c.979-9373G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 29 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 (SAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE3B	NM_000922.4	c.979-9373G>C		intron_variant	Intron 1 of 15	ENST00000282096.9	NP_000913.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE3B	ENST00000282096.9	c.979-9373G>C		intron_variant	Intron 1 of 15	1	NM_000922.4	ENSP00000282096.4
PDE3B	ENST00000455098.3	c.979-9373G>C		intron_variant	Intron 1 of 15	1		ENSP00000388644.2
PDE3B	ENST00000534317.1	n.795-9373G>C		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.141 AC: 5867 AN: 41496

American (AMR) AF: 0.461 AC: 7022 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1715 AN: 3466

East Asian (EAS) AF: 0.379 AC: 1952 AN: 5144

South Asian (SAS) AF: 0.465 AC: 2241 AN: 4820

European-Finnish (FIN) AF: 0.429 AC: 4528 AN: 10550

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.438 AC: 29726 AN: 67926

Other (OTH) AF: 0.367 AC: 774 AN: 2110

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
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11023332; hg19: chr11-14784110;