rs3792752

Variant summary

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

The NM_001204375.2(NPR3):​c.1060-6180A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,018 control chromosomes in the GnomAD database, including 7,818 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 0.31 ( 7818 hom., cov: 32)

Consequence

NPR3
NM_001204375.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.470
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NPR3NM_001204375.2 linkuse as main transcriptc.1060-6180A>G intron_variant ENST00000265074.13 NP_001191304.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NPR3ENST00000265074.13 linkuse as main transcriptc.1060-6180A>G intron_variant 1 NM_001204375.2 ENSP00000265074 P4P17342-1

Frequencies

GnomAD3 genomes
AF:
0.309
AC:
46926
AN:
151900
Hom.:
7816
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.439
Gnomad AMI
AF:
0.390
Gnomad AMR
AF:
0.295
Gnomad ASJ
AF:
0.279
Gnomad EAS
AF:
0.172
Gnomad SAS
AF:
0.271
Gnomad FIN
AF:
0.206
Gnomad MID
AF:
0.263
Gnomad NFE
AF:
0.263
Gnomad OTH
AF:
0.317
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.309
AC:
46965
AN:
152018
Hom.:
7818
Cov.:
32
AF XY:
0.305
AC XY:
22667
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.438
Gnomad4 AMR
AF:
0.294
Gnomad4 ASJ
AF:
0.279
Gnomad4 EAS
AF:
0.172
Gnomad4 SAS
AF:
0.271
Gnomad4 FIN
AF:
0.206
Gnomad4 NFE
AF:
0.263
Gnomad4 OTH
AF:
0.317
Alfa
AF:
0.269
Hom.:
9696
Bravo
AF:
0.317
Asia WGS
AF:
0.265
AC:
923
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
5.4
DANN
Benign
0.48

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: rs3792752; hg19: chr5-32768634; API