rs215614

chr7-32307723-G-A

Variant summary

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

The NM_001322059.2(PDE1C):c.311-98184C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,026 control chromosomes in the GnomAD database, including 29,801 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 0.62 (29801 hom., cov: 32)
• Consequence: PDE1C NM_001322059.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

Genes affected

PDE1C (HGNC:8776): (phosphodiesterase 1C) This gene encodes an enzyme that belongs to the 3'5'-cyclic nucleotide phosphodiesterase family. Members of this family catalyze hydrolysis of the cyclic nucleotides, cyclic adenosine monophosphate and cyclic guanosine monophosphate, to the corresponding nucleoside 5'-monophosphates. The enzyme encoded by this gene regulates proliferation and migration of vascular smooth muscle cells, and neointimal hyperplasia. This enzyme also plays a role in pathological vascular remodeling by regulating the stability of growth factor receptors, such as PDGF-receptor-beta. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE1C	NM_001322059.2	c.311-98184C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE1C	ENST00000672256.1	c.311-98184C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94399 AN: 151908 Hom.: 29771 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.622 AC: 94491 AN: 152026 Hom.: 29801 Cov.: 32 AF XY: 0.628 AC XY: 46625 AN XY: 74300

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.627

Alfa AF: 0.618 Hom.: 53086

Bravo AF: 0.614

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.71
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs215614; hg19: chr7-32347335;