rs10057069
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001204375.2(NPR3):c.769+3938T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 447,850 control chromosomes in the GnomAD database, including 12,225 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 0.23 ( 4167 hom., cov: 32)
Exomes 𝑓: 0.22 ( 8058 hom. )
Consequence
NPR3
NM_001204375.2 intron
NM_001204375.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.359
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPR3 | NM_001204375.2 | c.769+3938T>C | intron_variant | ENST00000265074.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPR3 | ENST00000265074.13 | c.769+3938T>C | intron_variant | 1 | NM_001204375.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.226 AC: 34405AN: 151972Hom.: 4174 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.219 AC: 64862AN: 295760Hom.: 8058 Cov.: 0 AF XY: 0.213 AC XY: 36020AN XY: 168874
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GnomAD4 genome ? AF: 0.226 AC: 34399AN: 152090Hom.: 4167 Cov.: 32 AF XY: 0.221 AC XY: 16412AN XY: 74338
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at