Variant 5-32710655-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001363652.2(NPR3):c.-8G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00682 in 1,501,148 control chromosomes in the GnomAD database, including 621 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.037 ( 359 hom., cov: 32)

Exomes 𝑓: 0.0034 ( 262 hom. )

Consequence

NPR3
NM_001363652.2 5_prime_UTR

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.52

Variant links:

Genes affected

NPR3 (HGNC:7945): (natriuretic peptide receptor 3) This gene encodes one of three natriuretic peptide receptors. Natriutetic peptides are small peptides which regulate blood volume and pressure, pulmonary hypertension, and cardiac function as well as some metabolic and growth processes. The product of this gene encodes a natriuretic peptide receptor responsible for clearing circulating and extracellular natriuretic peptides through endocytosis of the receptor. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]

NPR3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 5-32710655-G-A is Benign according to our data. Variant chr5-32710655-G-A is described in ClinVar as [Benign]. Clinvar id is 3044637.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	Protein	UniProt
NPR3	NM_001363652.2 link	c.-8G>A	5_prime_UTR_variant	1/8	NP_001350581.1
NPR3	NM_001204376.2 link	c.-8G>A	5_prime_UTR_variant	1/8	NP_001191305.1	P17342-3
NPR3	NM_001364460.2 link	c.-8G>A	5_prime_UTR_variant	1/7	NP_001351389.1
NPR3	NM_001364458.2 link	c.50-14043G>A	intron_variant		NP_001351387.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	UniProt
NPR3	ENST00000506712.1 link	n.2G>A	non_coding_transcript_exon_variant	1/6	1
NPR3	ENST00000434067 link	c.-8G>A	5_prime_UTR_variant	1/8	5	ENSP00000388408.2	C9JK69
NPR3	ENST00000326958 link	c.-8G>A	5_prime_UTR_variant	1/8	2	ENSP00000318340.2	P17342-3
NPR3	ENST00000509104.5 link	c.101-14043G>A	intron_variant		2	ENSP00000425325.1	D6RDL8

Frequencies

GnomAD3 genomes

AF:

0.0369

AC:

5605

AN:

152080

Hom.:

359

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00922

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000235

Gnomad OTH

AF:

0.0187

GnomAD3 exomes

AF:

0.00709

AC:

814

AN:

114874

Hom.:

AF XY:

0.00568

AC XY:

351

AN XY:

61776

show subpopulations

Gnomad AFR exome

AF:

0.134

Gnomad AMR exome

AF:

0.00571

Gnomad ASJ exome

AF:

0.000150

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000188

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000162

Gnomad OTH exome

AF:

0.00483

GnomAD4 exome

AF:

0.00343

AC:

4633

AN:

1348950

Hom.:

262

Cov.:

AF XY:

0.00297

AC XY:

1961

AN XY:

660084

show subpopulations

Gnomad4 AFR exome

AF:

0.131

Gnomad4 AMR exome

AF:

0.00658

Gnomad4 ASJ exome

AF:

0.0000426

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000252

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000779

Gnomad4 OTH exome

AF:

0.00773

GnomAD4 genome

AF:

0.0369

AC:

5611

AN:

152198

Hom.:

359

Cov.:

AF XY:

0.0346

AC XY:

2575

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.130

Gnomad4 AMR

AF:

0.00914

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000235

Gnomad4 OTH

AF:

0.0185

Alfa

AF:

0.0181

Hom.:

Bravo

AF:

0.0419

Asia WGS

AF:

0.00779

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

NPR3-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 30, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.88

Splicing

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