7-32188366-C-G

Variant names:

• chr7-32188366-C-G
• rs10263213
• NM_001191058.4:c.137-18410G>C

Variant summary

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

The NM_001191058.4(PDE1C):​c.137-18410G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,824 control chromosomes in the GnomAD database, including 9,666 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 0.34 (9666 hom., cov: 32)
• Consequence: PDE1C NM_001191058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

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 (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE1C	NM_001191058.4	c.137-18410G>C		intron_variant	Intron 2 of 18		NP_001177987.2
PDE1C	NM_001322059.2	c.362-18410G>C		intron_variant	Intron 2 of 17		NP_001308988.1
PDE1C	NM_001322058.2	c.137-18410G>C		intron_variant	Intron 2 of 17		NP_001308987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE1C	ENST00000396193.5	c.137-18410G>C		intron_variant	Intron 2 of 18	2		ENSP00000379496.1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51800 AN: 151706 Hom.: 9651 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.342 AC: 51860 AN: 151824 Hom.: 9666 Cov.: 32 AF XY: 0.342 AC XY: 25368 AN XY: 74222

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.322

Alfa AF: 0.172 Hom.: 357

Bravo AF: 0.356

Asia WGS AF: 0.352 AC: 1227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10263213; hg19: chr7-32227978;