rs2191876

Variant names:

• chr7-31843314-T-C
• rs2191876
• NM_001191057.4:c.980+4654A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-31843314-T-C
• chr7-31843314-T-G

Variant summary

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

The NM_001191057.4(PDE1C):​c.980+4654A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 151,778 control chromosomes in the GnomAD database, including 52,195 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 0.83 (52195 hom., cov: 31)
• Consequence: PDE1C NM_001191057.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE1C	NM_001191057.4	c.980+4654A>G		intron_variant	Intron 9 of 17	ENST00000396191.6	NP_001177986.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE1C	ENST00000396191.6	c.980+4654A>G		intron_variant	Intron 9 of 17	2	NM_001191057.4	ENSP00000379494.1

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125605 AN: 151660 Hom.: 52139 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.828 AC: 125721 AN: 151778 Hom.: 52195 Cov.: 31 AF XY: 0.832 AC XY: 61669 AN XY: 74150

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.813

Alfa AF: 0.819 Hom.: 11792

Bravo AF: 0.830

Asia WGS AF: 0.887 AC: 3071 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.40

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: rs2191876; hg19: chr7-31882928;