rs700926

Variant names:

• chr5-32745177-A-C
• rs700926
• NM_001204375.2:c.1059+6147A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-32745177-A-C
• chr5-32745177-A-G
• chr5-32745177-A-T

Variant summary

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

The NM_001204375.2(NPR3):​c.1059+6147A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,932 control chromosomes in the GnomAD database, including 8,822 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 0.32 (8822 hom., cov: 31)
• Consequence: NPR3 NM_001204375.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 4 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPR3	NM_001204375.2	c.1059+6147A>C		intron_variant	Intron 3 of 7	ENST00000265074.13	NP_001191304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPR3	ENST00000265074.13	c.1059+6147A>C		intron_variant	Intron 3 of 7	1	NM_001204375.2	ENSP00000265074.8

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49084 AN: 151810 Hom.: 8791 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.324 AC: 49172 AN: 151932 Hom.: 8822 Cov.: 31 AF XY: 0.322 AC XY: 23951 AN XY: 74272

African (AFR) AF: 0.488 AC: 20175 AN: 41384

American (AMR) AF: 0.309 AC: 4716 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 892 AN: 3464

East Asian (EAS) AF: 0.253 AC: 1306 AN: 5162

South Asian (SAS) AF: 0.346 AC: 1660 AN: 4802

European-Finnish (FIN) AF: 0.199 AC: 2109 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17234 AN: 67960

Other (OTH) AF: 0.291 AC: 615 AN: 2112

Alfa AF: 0.255 Hom.: 2436

Bravo AF: 0.336

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.39
PhyloP100		-0.25
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: rs700926; hg19: chr5-32745283;