rs2530566

Positions:

• chr7-34665211-A-G

Variant summary

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

The NM_207172.2(NPSR1):​c.147+6652A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,022 control chromosomes in the GnomAD database, including 24,832 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 0.55 (24832 hom., cov: 32)
• Consequence: NPSR1 NM_207172.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPSR1	NM_207172.2	c.147+6652A>G		intron_variant		ENST00000360581.6	NP_997055.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPSR1	ENST00000360581.6	c.147+6652A>G		intron_variant		1	NM_207172.2	ENSP00000353788.1

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84060 AN: 151904 Hom.: 24795 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.554 AC: 84151 AN: 152022 Hom.: 24832 Cov.: 32 AF XY: 0.552 AC XY: 41004 AN XY: 74324

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.560

Alfa AF: 0.516 Hom.: 3367

Bravo AF: 0.566

Asia WGS AF: 0.438 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.41

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

Other links and lift over

dbSNP: rs2530566; hg19: chr7-34704823;