Variant chr7-31809149-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001191057.4(PDE1C):c.1814-41A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0477 in 1,086,620 control chromosomes in the GnomAD database, including 1,379 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.047 ( 192 hom., cov: 32)

Exomes 𝑓: 0.048 ( 1187 hom. )

Consequence

PDE1C
NM_001191057.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.679

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 -14 ACMG points.

BP4

This place is a probable branch point but likely benign (scored 2 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 7-31809149-T-C is Benign according to our data. Variant chr7-31809149-T-C is described in ClinVar as [Benign]. Clinvar id is 1273421.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0682 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.1814-41A>G		intron_variant		ENST00000396191.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE1C	ENST00000396191.6 linkuse as main transcript	c.1814-41A>G		intron_variant		2	NM_001191057.4	A1	Q14123-1

Frequencies

GnomAD3 genomes

AF:

0.0470

AC:

7151

AN:

151992

Hom.:

192

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0462

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.0298

Gnomad ASJ

AF:

0.0236

Gnomad EAS

AF:

0.0425

Gnomad SAS

AF:

0.0743

Gnomad FIN

AF:

0.0744

Gnomad MID

AF:

0.0446

Gnomad NFE

AF:

0.0472

Gnomad OTH

AF:

0.0439

GnomAD3 exomes

AF:

0.0489

AC:

11597

AN:

237154

Hom.:

336

AF XY:

0.0508

AC XY:

6506

AN XY:

128050

show subpopulations

Gnomad AFR exome

AF:

0.0483

Gnomad AMR exome

AF:

0.0188

Gnomad ASJ exome

AF:

0.0247

Gnomad EAS exome

AF:

0.0454

Gnomad SAS exome

AF:

0.0762

Gnomad FIN exome

AF:

0.0775

Gnomad NFE exome

AF:

0.0485

Gnomad OTH exome

AF:

0.0450

GnomAD4 exome

AF:

0.0477

AC:

44621

AN:

934506

Hom.:

1187

Cov.:

AF XY:

0.0487

AC XY:

23715

AN XY:

487258

show subpopulations

Gnomad4 AFR exome

AF:

0.0478

Gnomad4 AMR exome

AF:

0.0192

Gnomad4 ASJ exome

AF:

0.0253

Gnomad4 EAS exome

AF:

0.0292

Gnomad4 SAS exome

AF:

0.0722

Gnomad4 FIN exome

AF:

0.0729

Gnomad4 NFE exome

AF:

0.0466

Gnomad4 OTH exome

AF:

0.0463

GnomAD4 genome

AF:

0.0471

AC:

7162

AN:

152114

Hom.:

192

Cov.:

AF XY:

0.0481

AC XY:

3573

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.0461

Gnomad4 AMR

AF:

0.0298

Gnomad4 ASJ

AF:

0.0236

Gnomad4 EAS

AF:

0.0422

Gnomad4 SAS

AF:

0.0746

Gnomad4 FIN

AF:

0.0744

Gnomad4 NFE

AF:

0.0472

Gnomad4 OTH

AF:

0.0463

Alfa

AF:

0.0446

Hom.:

Bravo

AF:

0.0419

Asia WGS

AF:

0.0590

AC:

206

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.85

BranchPoint Hunter

2.0

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