7-31864413-C-T

Position:

• chr7-31864413-C-T

Variant summary

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

The NM_001191057.4(PDE1C):​c.750+529G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,852 control chromosomes in the GnomAD database, including 6,965 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 0.30 (6965 hom., cov: 33)
• Consequence: PDE1C NM_001191057.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

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]

PDE1C (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE1C	NM_001191057.4	c.750+529G>A		intron_variant		ENST00000396191.6	NP_001177986.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE1C	ENST00000396191.6	c.750+529G>A		intron_variant		2	NM_001191057.4	ENSP00000379494.1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45343 AN: 151732 Hom.: 6956 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.299 AC: 45391 AN: 151852 Hom.: 6965 Cov.: 33 AF XY: 0.299 AC XY: 22199 AN XY: 74216

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.329

Alfa AF: 0.282 Hom.: 12666

Bravo AF: 0.308

Asia WGS AF: 0.314 AC: 1089 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	0.041
DANN	Benign	0.63

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: rs2270221; hg19: chr7-31904027;