chr7-31790481-A-G

Position:

• chr7-31790481-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.1892-14749T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,960 control chromosomes in the GnomAD database, including 23,727 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.54 (23727 hom., cov: 31)
• Consequence: PDE1C NM_001191057.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.767

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=-0.81).
• BP6: Variant 7-31790481-A-G is Benign according to our data. Variant chr7-31790481-A-G is described in ClinVar as [Benign]. Clinvar id is 1273656.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE1C	NM_001191057.4	c.1892-14749T>C		intron_variant		ENST00000396191.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE1C	ENST00000396191.6	c.1892-14749T>C		intron_variant		2	NM_001191057.4	A1

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82026 AN: 151842 Hom.: 23718 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.551

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.540 AC: 82039 AN: 151960 Hom.: 23727 Cov.: 31 AF XY: 0.543 AC XY: 40373 AN XY: 74284

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.548

Alfa AF: 0.612 Hom.: 28183

Bravo AF: 0.527

Asia WGS AF: 0.583 AC: 2027 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 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.85

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: rs982857; hg19: chr7-31830095;