chr7-31815781-A-G

Position:

• chr7-31815781-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+143T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00572 in 671,590 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.018 (72 hom., cov: 32)
  • Exomes 𝑓: 0.0022 (27 hom.)
• Consequence: PDE1C NM_001191057.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.434

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=-0.93).
• BP6: Variant 7-31815781-A-G is Benign according to our data. Variant chr7-31815781-A-G is described in ClinVar as [Benign]. Clinvar id is 1286911.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE1C	NM_001191057.4	c.1813+143T>C		intron_variant		ENST00000396191.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE1C	ENST00000396191.6	c.1813+143T>C		intron_variant		2	NM_001191057.4	A1

Frequencies

GnomAD3 genomes AF: 0.0177 AC: 2690 AN: 152048 Hom.: 72 Cov.: 32

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00485

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000382

Gnomad OTH AF: 0.00955

GnomAD4 exome AF: 0.00221 AC: 1147 AN: 519424 Hom.: 27 AF XY: 0.00184 AC XY: 509 AN XY: 277122

Gnomad4 AFR exome AF: 0.0586

Gnomad4 AMR exome AF: 0.00260

Gnomad4 ASJ exome AF: 0.000879

Gnomad4 EAS exome AF: 0.0000293

Gnomad4 SAS exome AF: 0.000177

Gnomad4 FIN exome AF: 0.0000250

Gnomad4 NFE exome AF: 0.000291

Gnomad4 OTH exome AF: 0.00416

GnomAD4 genome AF: 0.0177 AC: 2692 AN: 152166 Hom.: 72 Cov.: 32 AF XY: 0.0176 AC XY: 1309 AN XY: 74406

Gnomad4 AFR AF: 0.0618

Gnomad4 AMR AF: 0.00484

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000382

Gnomad4 OTH AF: 0.00945

Alfa AF: 0.0146 Hom.: 2

Bravo AF: 0.0203

Asia WGS AF: 0.00260 AC: 10 AN: 3478

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 22, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.59

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: rs73319150; hg19: chr7-31855395;