NPSR1 p.Asn107Ile

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is The variant received -5 classification points (ACGS-UK Somatic Oncogenicity v2025): 0P and 5B. B1_StrongB3_Supporting

The NM_207172.2(NPSR1):c.320A>T (p.Asn107Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.45 (AC=723,701) in the gnomAD database across 1,609,296 control chromosomes, including 165,204 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.538. In-silico predictor (REVEL) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign/Likely Benign (no review stars). The variant has been observed in cBioPortal in 3 samples across 3 studies and 3 cancer types; somatic enrichment level: SUPPORTING_LOW (Observed in a small number of cBioPortal cases.). This exact variant is curated in the UniProt human variants database as Uncertain Significance; it is also listed as a COSMIC curated somatic variant.

Frequency

Genomes: 𝑓 0.47 ( 17297 hom., cov: 32)

Exomes 𝑓: 0.45 ( 147907 hom. )

Consequence

NPSR1
NM_207172.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 3.31

Publications

137 publications found

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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_207172.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 points.

GnomAD effective popmax AF >1% — B1 stand-alone benign; GnomAD effective popmax AF = 0.538 — exceeds 1% threshold (B1 applied)

Computational evidence does not support a deleterious effect; Missense variant — primary computational scorer does not support an oncogenic/deleterious effect; supports B3

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_207172.2. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NPSR1	NM_207172.2	MANE Select	c.320A>T	p.Asn107Ile	missense	Exon 3 of 9	NP_997055.1	Q6W5P4-1
NPSR1	NM_001300935.2		c.320A>T	p.Asn107Ile	missense	Exon 3 of 10	NP_001287864.1	Q6W5P4-3
NPSR1	NM_207173.2		c.320A>T	p.Asn107Ile	missense	Exon 3 of 9	NP_997056.1	Q6W5P4-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NPSR1	ENST00000360581.6	TSL:1 MANE Select	c.320A>T	p.Asn107Ile	missense	Exon 3 of 9	ENSP00000353788.1	Q6W5P4-1
NPSR1	ENST00000381539.3	TSL:1	c.320A>T	p.Asn107Ile	missense	Exon 3 of 10	ENSP00000370950.3	Q6W5P4-3
NPSR1	ENST00000359791.5	TSL:1	c.320A>T	p.Asn107Ile	missense	Exon 3 of 9	ENSP00000352839.1	Q6W5P4-4

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71686

AN:

151878

Hom.:

17289

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.437

Gnomad AMR

AF:

0.385

Gnomad ASJ

AF:

0.428

Gnomad EAS

AF:

0.541

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.487

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.455

Gnomad OTH

AF:

0.460

GnomAD2 exomes

AF:

0.437

AC:

109388

AN:

250250

AF XY:

0.432

show subpopulations

Gnomad AFR exome

AF:

0.543

Gnomad AMR exome

AF:

0.340

Gnomad ASJ exome

AF:

0.433

Gnomad EAS exome

AF:

0.528

Gnomad FIN exome

AF:

0.475

Gnomad NFE exome

AF:

0.459

Gnomad OTH exome

AF:

0.432

GnomAD4 exome

AF:

0.447

AC:

651975

AN:

1457300

Hom.:

147907

Cov.:

AF XY:

0.444

AC XY:

322307

AN XY:

725206

show subpopulations

African (AFR)

AF:

0.545

AC:

18146

AN:

33308

American (AMR)

AF:

0.345

AC:

15363

AN:

44504

Ashkenazi Jewish (ASJ)

AF:

0.430

AC:

11203

AN:

26072

East Asian (EAS)

AF:

0.531

AC:

21007

AN:

39598

South Asian (SAS)

AF:

0.331

AC:

28503

AN:

86050

European-Finnish (FIN)

AF:

0.473

AC:

25222

AN:

53344

Middle Eastern (MID)

AF:

0.430

AC:

2475

AN:

5752

European-Non Finnish (NFE)

AF:

0.454

AC:

503250

AN:

1108464

Other (OTH)

AF:

0.445

AC:

26806

AN:

60208

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

15686

31373

47059

62746

78432

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15028

30056

45084

60112

75140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.472

AC:

71726

AN:

151996

Hom.:

17297

Cov.:

AF XY:

0.469

AC XY:

34855

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.540

AC:

22386

AN:

41444

American (AMR)

AF:

0.384

AC:

5863

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.428

AC:

1486

AN:

3468

East Asian (EAS)

AF:

0.541

AC:

2787

AN:

5148

South Asian (SAS)

AF:

0.337

AC:

1622

AN:

4820

European-Finnish (FIN)

AF:

0.487

AC:

5145

AN:

10564

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.455

AC:

30942

AN:

67970

Other (OTH)

AF:

0.459

AC:

969

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1937

3874

5812

7749

9686

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.455

Hom.:

12295

Bravo

AF:

0.473

Asia WGS

AF:

0.425

AC:

1477

AN:

3478

EpiCase

AF:

0.452

EpiControl

AF:

0.452

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.535

AC:

65685

AN:

122712

Turkish Variome

AF:

0.435

AC:

2925

AN:

6720

Hom.:

658

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.532

AC:

4767

AN:

8960

Hom.:

1263

ABraOM SABE-WGS-1171

AF:

0.427

AC:

999

AN:

2342

Hom.:

225

ClinVar

ClinVar submissions

Significance:Benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

Asthma-related traits, susceptibility to, 2 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.021

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.41

CADD

Benign

(source)

DANN

Benign

0.77

DEOGEN2

Benign

0.048

Eigen

Benign

-1.1

Eigen_PC

Benign

-0.91

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.068

MetaRNN

Benign

0.00059

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-2.5

PhyloP100

3.3

PrimateAI

Uncertain

0.75

PROVEAN

Benign

5.7

REVEL

Benign

0.12

Sift

Benign

1.0

Sift4G

Benign

1.0

Varity_R

0.15

gMVP

0.10

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over