Variant 7-31809092-A-G 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.1830T>C(p.Gly610=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 1,582,904 control chromosomes in the GnomAD database, including 30,873 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3092 hom., cov: 32)

Exomes 𝑓: 0.19 ( 27781 hom. )

Consequence

PDE1C
NM_001191057.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0620

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=-0.51).

BP6

Variant 7-31809092-A-G is Benign according to our data. Variant chr7-31809092-A-G is described in ClinVar as [Benign]. Clinvar id is 1241492.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.062 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 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.1830T>C	p.Gly610=	synonymous_variant	16/18	ENST00000396191.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE1C	ENST00000396191.6 linkuse as main transcript	c.1830T>C	p.Gly610=	synonymous_variant	16/18	2	NM_001191057.4	A1	Q14123-1

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30170

AN:

151776

Hom.:

3093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.192

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.215

GnomAD3 exomes

AF:

0.193

AC:

48076

AN:

248792

Hom.:

4947

AF XY:

0.199

AC XY:

26729

AN XY:

134496

show subpopulations

Gnomad AFR exome

AF:

0.214

Gnomad AMR exome

AF:

0.141

Gnomad ASJ exome

AF:

0.306

Gnomad EAS exome

AF:

0.136

Gnomad SAS exome

AF:

0.239

Gnomad FIN exome

AF:

0.139

Gnomad NFE exome

AF:

0.203

Gnomad OTH exome

AF:

0.208

GnomAD4 exome

AF:

0.193

AC:

275697

AN:

1431010

Hom.:

27781

Cov.:

AF XY:

0.195

AC XY:

139424

AN XY:

713878

show subpopulations

Gnomad4 AFR exome

AF:

0.212

Gnomad4 AMR exome

AF:

0.148

Gnomad4 ASJ exome

AF:

0.307

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.239

Gnomad4 FIN exome

AF:

0.142

Gnomad4 NFE exome

AF:

0.191

Gnomad4 OTH exome

AF:

0.208

GnomAD4 genome

AF:

0.199

AC:

30194

AN:

151894

Hom.:

3092

Cov.:

AF XY:

0.195

AC XY:

14468

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.211

Gnomad4 AMR

AF:

0.192

Gnomad4 ASJ

AF:

0.315

Gnomad4 EAS

AF:

0.135

Gnomad4 SAS

AF:

0.224

Gnomad4 FIN

AF:

0.139

Gnomad4 NFE

AF:

0.200

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.208

Hom.:

5797

Bravo

AF:

0.204

Asia WGS

AF:

0.157

AC:

545

AN:

3474

EpiCase

AF:

0.215

EpiControl

AF:

0.221

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

-0.51

CADD

Benign

6.2

DANN

Benign

0.76

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