5-32709113-G-A

Variant names:

• chr5-32709113-G-A
• rs764124
• NM_001364458.2:c.50-15585G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001364458.2(NPR3):​c.50-15585G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,928 control chromosomes in the GnomAD database, including 3,237 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3237 hom., cov: 30)
• Consequence: NPR3 NM_001364458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 2 publications found

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 Gene-Disease associations (from GenCC):

• Boudin-Mortier syndrome

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPR3	NM_001364458.2	c.50-15585G>A		intron_variant	Intron 1 of 7		NP_001351387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPR3	ENST00000509104.5	c.101-15585G>A		intron_variant	Intron 1 of 5	2		ENSP00000425325.1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30074 AN: 151810 Hom.: 3242 Cov.: 30

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.198 AC: 30054 AN: 151928 Hom.: 3237 Cov.: 30 AF XY: 0.195 AC XY: 14477 AN XY: 74266

African (AFR) AF: 0.156 AC: 6448 AN: 41406

American (AMR) AF: 0.157 AC: 2397 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3466

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5180

South Asian (SAS) AF: 0.106 AC: 511 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2454 AN: 10568

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16596 AN: 67930

Other (OTH) AF: 0.225 AC: 475 AN: 2110

Alfa AF: 0.218 Hom.: 978

Bravo AF: 0.190

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.79
PhyloP100		-0.43
PromoterAI		-0.0048	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs764124; hg19: chr5-32709219;