Variant 7-31815955-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001191057.4(PDE1C):c.1782C>T(p.Ala594=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 1,612,540 control chromosomes in the GnomAD database, including 46,070 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4217 hom., cov: 32)

Exomes 𝑓: 0.23 ( 41853 hom. )

Consequence

PDE1C
NM_001191057.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.35

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 7-31815955-G-A is Benign according to our data. Variant chr7-31815955-G-A is described in ClinVar as [Benign]. Clinvar id is 1234874.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.35 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE1C	NM_001191057.4 linkuse as main transcript	c.1782C>T	p.Ala594=	synonymous_variant	15/18	ENST00000396191.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE1C	ENST00000396191.6 linkuse as main transcript	c.1782C>T	p.Ala594=	synonymous_variant	15/18	2	NM_001191057.4	A1	Q14123-1

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35325

AN:

151916

Hom.:

4219

Cov.:

show subpopulations

Gnomad AFR

AF:

0.227

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.210

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.243

Gnomad OTH

AF:

0.267

GnomAD3 exomes

AF:

0.231

AC:

58170

AN:

251362

Hom.:

7397

AF XY:

0.240

AC XY:

32571

AN XY:

135854

show subpopulations

Gnomad AFR exome

AF:

0.234

Gnomad AMR exome

AF:

0.141

Gnomad ASJ exome

AF:

0.354

Gnomad EAS exome

AF:

0.169

Gnomad SAS exome

AF:

0.302

Gnomad FIN exome

AF:

0.170

Gnomad NFE exome

AF:

0.249

Gnomad OTH exome

AF:

0.252

GnomAD4 exome

AF:

0.235

AC:

342782

AN:

1460506

Hom.:

41853

Cov.:

AF XY:

0.238

AC XY:

173168

AN XY:

726626

show subpopulations

Gnomad4 AFR exome

AF:

0.229

Gnomad4 AMR exome

AF:

0.150

Gnomad4 ASJ exome

AF:

0.357

Gnomad4 EAS exome

AF:

0.178

Gnomad4 SAS exome

AF:

0.297

Gnomad4 FIN exome

AF:

0.170

Gnomad4 NFE exome

AF:

0.234

Gnomad4 OTH exome

AF:

0.246

GnomAD4 genome

AF:

0.232

AC:

35335

AN:

152034

Hom.:

4217

Cov.:

AF XY:

0.227

AC XY:

16873

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.227

Gnomad4 AMR

AF:

0.210

Gnomad4 ASJ

AF:

0.365

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.284

Gnomad4 FIN

AF:

0.174

Gnomad4 NFE

AF:

0.243

Gnomad4 OTH

AF:

0.264

Alfa

AF:

0.251

Hom.:

8559

Bravo

AF:

0.234

Asia WGS

AF:

0.208

AC:

725

AN:

3476

EpiCase

AF:

0.266

EpiControl

AF:

0.270

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 04, 2021

- -

Hearing loss, autosomal dominant 74

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.31

DANN

Benign

0.80

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over