rs1847018

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001204375.2(NPR3):​c.769+2010C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 150,024 control chromosomes in the GnomAD database, including 1,210 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 0.12 ( 1210 hom., cov: 32)

Consequence

NPR3
NM_001204375.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.720
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NPR3NM_001204375.2 linkuse as main transcriptc.769+2010C>T intron_variant ENST00000265074.13 NP_001191304.1 P17342-1A8K4A5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NPR3ENST00000265074.13 linkuse as main transcriptc.769+2010C>T intron_variant 1 NM_001204375.2 ENSP00000265074.8 P17342-1

Frequencies

GnomAD3 genomes
AF:
0.124
AC:
18565
AN:
149920
Hom.:
1207
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.109
Gnomad AMI
AF:
0.113
Gnomad AMR
AF:
0.202
Gnomad ASJ
AF:
0.108
Gnomad EAS
AF:
0.107
Gnomad SAS
AF:
0.0832
Gnomad FIN
AF:
0.119
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.122
Gnomad OTH
AF:
0.112
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.124
AC:
18579
AN:
150024
Hom.:
1210
Cov.:
32
AF XY:
0.125
AC XY:
9147
AN XY:
73050
show subpopulations
Gnomad4 AFR
AF:
0.109
Gnomad4 AMR
AF:
0.202
Gnomad4 ASJ
AF:
0.108
Gnomad4 EAS
AF:
0.107
Gnomad4 SAS
AF:
0.0839
Gnomad4 FIN
AF:
0.119
Gnomad4 NFE
AF:
0.122
Gnomad4 OTH
AF:
0.110
Alfa
AF:
0.128
Hom.:
229
Bravo
AF:
0.129
Asia WGS
AF:
0.0840
AC:
295
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
8.5
DANN
Benign
0.70

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1847018; hg19: chr5-32714661; API