chr5-32771832-A-G

Variant names:

• chr5-32771832-A-G
• rs1173736
• NM_001204375.2:c.1060-2876A>G

Variant summary

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

The NM_001204375.2(NPR3):​c.1060-2876A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,884 control chromosomes in the GnomAD database, including 13,784 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 0.38 (13784 hom., cov: 31)
• Consequence: NPR3 NM_001204375.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001204375.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPR3	NM_001204375.2	MANE Select	c.1060-2876A>G		intron	N/A	NP_001191304.1
	NPR3	NM_000908.4		c.1060-2876A>G		intron	N/A	NP_000899.1
	NPR3	NM_001363652.2		c.412-2876A>G		intron	N/A	NP_001350581.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPR3	ENST00000265074.13	TSL:1 MANE Select	c.1060-2876A>G		intron	N/A	ENSP00000265074.8
	NPR3	ENST00000415167.2	TSL:1	c.1060-2876A>G		intron	N/A	ENSP00000398028.2
	NPR3	ENST00000506712.1	TSL:1	n.421-2876A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57660 AN: 151766 Hom.: 13748 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.380 AC: 57750 AN: 151884 Hom.: 13784 Cov.: 31 AF XY: 0.375 AC XY: 27814 AN XY: 74246

African (AFR) AF: 0.687 AC: 28422 AN: 41384

American (AMR) AF: 0.317 AC: 4844 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3468

East Asian (EAS) AF: 0.176 AC: 909 AN: 5164

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4816

European-Finnish (FIN) AF: 0.206 AC: 2180 AN: 10562

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17880 AN: 67920

Other (OTH) AF: 0.366 AC: 770 AN: 2104

Alfa AF: 0.291 Hom.: 8532

Bravo AF: 0.397

Asia WGS AF: 0.286 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.56
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1173736; hg19: chr5-32771938;