rs7116978

chr11-14860225-T-C

Variant summary

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

The NM_000922.4(PDE3B):c.2724+979T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,982 control chromosomes in the GnomAD database, including 32,311 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 (32311 hom., cov: 32)
• Consequence: PDE3B NM_000922.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

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 (AMR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE3B	NM_000922.4	c.2724+979T>C		intron_variant		ENST00000282096.9
PDE3B	NM_001363569.2	c.2571+979T>C		intron_variant
PDE3B	NM_001363570.2	c.2958+979T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE3B	ENST00000282096.9	c.2724+979T>C		intron_variant		1	NM_000922.4	P2
PDE3B	ENST00000455098.2	c.2571+979T>C		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98819 AN: 151864 Hom.: 32265 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.651 AC: 98927 AN: 151982 Hom.: 32311 Cov.: 32 AF XY: 0.657 AC XY: 48788 AN XY: 74282

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.656

Alfa AF: 0.658 Hom.: 20206

Bravo AF: 0.656

Asia WGS AF: 0.651 AC: 2259 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.6
Dann	Benign	0.74

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: rs7116978; hg19: chr11-14881771;