rs1833090

Variant names:

• chr7-34868174-A-C
• rs1833090
• ENST00000359791.5:c.1026-9902A>C

Your query was ambiguous. Multiple possible variants found:

• chr7-34868174-A-C
• chr7-34868174-A-G
• chr7-34868174-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207173.2(NPSR1):​c.1026-9902A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 151,388 control chromosomes in the GnomAD database, including 45,692 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 0.77 (45692 hom., cov: 30)
• Consequence: NPSR1 NM_207173.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.87

Genes affected

NPSR1 (HGNC:23631): (neuropeptide S receptor 1) This gene encodes a member of the vasopressin/oxytocin subfamily of G protein-coupled receptors. The encoded membrane protein acts as a receptor for neuropeptide S and affects a variety of cellular processes through its signaling. Increased expression of this gene in ciliated cells of the respiratory epithelium and in bronchial smooth muscle cells is associated with asthma. Polymorphisms in this gene have also been associated with asthma susceptibility, panic disorders, inflammatory bowel disease, and rheumatoid arthritis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

NPSR1-AS1 (HGNC:22128): (NPSR1 antisense RNA 1) This gene is located within a region that has been associated with asthma susceptibility. The locus is considered non-protein-coding based on lack of protein homology and a lack of experimental support for an encoded protein. Three alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPSR1	NM_207173.2	c.1026-9902A>C		intron_variant	Intron 8 of 8		NP_997056.1
NPSR1	NM_001300933.2	c.993-9902A>C		intron_variant	Intron 8 of 8		NP_001287862.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPSR1	ENST00000359791.5	c.1026-9902A>C		intron_variant	Intron 8 of 8	1		ENSP00000352839.1
NPSR1	ENST00000531252.5	c.993-9902A>C		intron_variant	Intron 8 of 8	1		ENSP00000433258.1
NPSR1-AS1	ENST00000431669.5	n.84+3325T>G		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.771 AC: 116654 AN: 151268 Hom.: 45635 Cov.: 30

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.771 AC: 116769 AN: 151388 Hom.: 45692 Cov.: 30 AF XY: 0.772 AC XY: 57101 AN XY: 73990

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.747

Alfa AF: 0.725 Hom.: 49837

Bravo AF: 0.769

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.18
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1833090; hg19: chr7-34907786;