chr7-31815806-A-G

Position:

• chr7-31815806-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001191057.4(PDE1C):​c.1813+118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 761,522 control chromosomes in the GnomAD database, including 351,836 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.95 (69084 hom., cov: 30)
  • Exomes 𝑓: 0.96 (282752 hom.)
• Consequence: PDE1C NM_001191057.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.261

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 7-31815806-A-G is Benign according to our data. Variant chr7-31815806-A-G is described in ClinVar as [Benign]. Clinvar id is 1222336.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE1C	NM_001191057.4	c.1813+118T>C		intron_variant		ENST00000396191.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE1C	ENST00000396191.6	c.1813+118T>C		intron_variant		2	NM_001191057.4	A1

Frequencies

GnomAD3 genomes AF: 0.953 AC: 144850 AN: 152048 Hom.: 69039 Cov.: 30

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.950

GnomAD4 exome AF: 0.963 AC: 586906 AN: 609356 Hom.: 282752 AF XY: 0.963 AC XY: 311727 AN XY: 323614

Gnomad4 AFR exome AF: 0.915

Gnomad4 AMR exome AF: 0.976

Gnomad4 ASJ exome AF: 0.947

Gnomad4 EAS exome AF: 0.925

Gnomad4 SAS exome AF: 0.960

Gnomad4 FIN exome AF: 0.989

Gnomad4 NFE exome AF: 0.967

Gnomad4 OTH exome AF: 0.959

GnomAD4 genome AF: 0.953 AC: 144954 AN: 152166 Hom.: 69084 Cov.: 30 AF XY: 0.955 AC XY: 70994 AN XY: 74374

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.965

Gnomad4 ASJ AF: 0.947

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.966

Gnomad4 OTH AF: 0.950

Alfa AF: 0.958 Hom.: 14903

Bravo AF: 0.949

Asia WGS AF: 0.938 AC: 3259 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1860789; hg19: chr7-31855420;