Variant rs887020 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_207172.2(NPSR1):c.-43A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 1,606,998 control chromosomes in the GnomAD database, including 244,310 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 0.45 ( 17835 hom., cov: 33)

Exomes 𝑓: 0.55 ( 226475 hom. )

Consequence

NPSR1
NM_207172.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.20

Variant links:

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 links:

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]

NPSR1-AS1 links:

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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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPSR1	NM_207172.2 linkuse as main transcript	c.-43A>G		5_prime_UTR_variant	1/9	ENST00000360581.6	NP_997055.1
NPSR1-AS1	NR_033665.1 linkuse as main transcript	n.279+70367T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPSR1	ENST00000360581.6 linkuse as main transcript	c.-43A>G		5_prime_UTR_variant	1/9	1	NM_207172.2	ENSP00000353788	P1	Q6W5P4-1
NPSR1-AS1	ENST00000419766.5 linkuse as main transcript	n.241+70367T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.447

AC:

68033

AN:

152036

Hom.:

17822

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.597

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.788

Gnomad SAS

AF:

0.573

Gnomad FIN

AF:

0.543

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.554

Gnomad OTH

AF:

0.440

GnomAD3 exomes

AF:

0.543

AC:

133903

AN:

246668

Hom.:

38375

AF XY:

0.548

AC XY:

72995

AN XY:

133182

show subpopulations

Gnomad AFR exome

AF:

0.158

Gnomad AMR exome

AF:

0.579

Gnomad ASJ exome

AF:

0.465

Gnomad EAS exome

AF:

0.790

Gnomad SAS exome

AF:

0.568

Gnomad FIN exome

AF:

0.547

Gnomad NFE exome

AF:

0.547

Gnomad OTH exome

AF:

0.530

GnomAD4 exome

AF:

0.552

AC:

803026

AN:

1454844

Hom.:

226475

Cov.:

AF XY:

0.553

AC XY:

399967

AN XY:

723346

show subpopulations

Gnomad4 AFR exome

AF:

0.147

Gnomad4 AMR exome

AF:

0.569

Gnomad4 ASJ exome

AF:

0.467

Gnomad4 EAS exome

AF:

0.796

Gnomad4 SAS exome

AF:

0.566

Gnomad4 FIN exome

AF:

0.556

Gnomad4 NFE exome

AF:

0.557

Gnomad4 OTH exome

AF:

0.534

GnomAD4 genome

AF:

0.447

AC:

68072

AN:

152154

Hom.:

17835

Cov.:

AF XY:

0.452

AC XY:

33594

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.168

Gnomad4 AMR

AF:

0.497

Gnomad4 ASJ

AF:

0.471

Gnomad4 EAS

AF:

0.788

Gnomad4 SAS

AF:

0.573

Gnomad4 FIN

AF:

0.543

Gnomad4 NFE

AF:

0.554

Gnomad4 OTH

AF:

0.441

Alfa

AF:

0.530

Hom.:

27968

Bravo

AF:

0.429

Asia WGS

AF:

0.626

AC:

2178

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.087

DANN

Benign

0.47

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over