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GeneBe

rs887020

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

2

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-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]

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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 UniProt
NPSR1NM_207172.2 linkuse as main transcriptc.-43A>G 5_prime_UTR_variant 1/9 ENST00000360581.6
NPSR1-AS1NR_033665.1 linkuse as main transcriptn.279+70367T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NPSR1ENST00000360581.6 linkuse as main transcriptc.-43A>G 5_prime_UTR_variant 1/91 NM_207172.2 P1Q6W5P4-1
NPSR1-AS1ENST00000419766.5 linkuse as main transcriptn.241+70367T>C intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.447
AC:
68033
AN:
152036
Hom.:
17822
Cov.:
33
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.:
33
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.:
33
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.

Other links and lift over

dbSNP: rs887020; hg19: chr7-34697982; COSMIC: COSV62199271; COSMIC: COSV62199271; API