rs3792758

chr5-32745646-C-Achr5-32745646-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001204375.2(NPR3):c.1059+6616C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,006 control chromosomes in the GnomAD database, including 10,172 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 0.35 (10172 hom., cov: 32)
• Consequence: NPR3 NM_001204375.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPR3	NM_001204375.2	c.1059+6616C>A		intron_variant		ENST00000265074.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPR3	ENST00000265074.13	c.1059+6616C>A		intron_variant		1	NM_001204375.2	P4

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53187 AN: 151890 Hom.: 10137 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.350 AC: 53263 AN: 152006 Hom.: 10172 Cov.: 32 AF XY: 0.349 AC XY: 25966 AN XY: 74336

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.345

Alfa AF: 0.286 Hom.: 9070

Bravo AF: 0.358

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.99
Dann	Benign	0.51

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: rs3792758; hg19: chr5-32745752;