5-32711547-A-ACTTTTT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001204375.2(NPR3):c.-211_-206dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 965,810 control chromosomes in the GnomAD database, including 401,897 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.95 (67285 hom., cov: 0)
  • Exomes 𝑓: 0.91 (334612 hom.)
• Consequence: NPR3 NM_001204375.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.914

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-32711547-A-ACTTTTT is Benign according to our data. Variant chr5-32711547-A-ACTTTTT is described in ClinVar as [Benign]. Clinvar id is 1294893.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPR3	NM_001204375.2	c.-211_-206dup		5_prime_UTR_variant	1/8	ENST00000265074.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPR3	ENST00000265074.13	c.-211_-206dup		5_prime_UTR_variant	1/8	1	NM_001204375.2	P4

Frequencies

GnomAD3 genomes AF: 0.952 AC: 140852 AN: 147886 Hom.: 67259 Cov.: 0

Gnomad AFR AF: 0.884

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.965

GnomAD4 exome AF: 0.909 AC: 743216 AN: 817828 Hom.: 334612 Cov.: 27 AF XY: 0.908 AC XY: 350829 AN XY: 386216

Gnomad4 AFR exome AF: 0.799

Gnomad4 AMR exome AF: 0.811

Gnomad4 ASJ exome AF: 0.902

Gnomad4 EAS exome AF: 0.854

Gnomad4 SAS exome AF: 0.915

Gnomad4 FIN exome AF: 0.897

Gnomad4 NFE exome AF: 0.915

Gnomad4 OTH exome AF: 0.893

GnomAD4 genome AF: 0.952 AC: 140926 AN: 147982 Hom.: 67285 Cov.: 0 AF XY: 0.952 AC XY: 68492 AN XY: 71952

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.996

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.994

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.991

Gnomad4 OTH AF: 0.963

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs59057102; hg19: chr5-32711653;