7-34666794-A-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_207172.2(NPSR1):​c.147+8235A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,836 control chromosomes in the GnomAD database, including 8,446 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 0.30 ( 8446 hom., cov: 31)

Consequence

NPSR1
NM_207172.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.162

Publications

5 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-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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NPSR1NM_207172.2 linkc.147+8235A>C intron_variant Intron 1 of 8 ENST00000360581.6 NP_997055.1 Q6W5P4-1A0A090N8Z1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NPSR1ENST00000360581.6 linkc.147+8235A>C intron_variant Intron 1 of 8 1 NM_207172.2 ENSP00000353788.1 Q6W5P4-1

Frequencies

GnomAD3 genomes
AF:
0.304
AC:
46129
AN:
151718
Hom.:
8434
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.522
Gnomad AMI
AF:
0.246
Gnomad AMR
AF:
0.203
Gnomad ASJ
AF:
0.276
Gnomad EAS
AF:
0.183
Gnomad SAS
AF:
0.215
Gnomad FIN
AF:
0.248
Gnomad MID
AF:
0.275
Gnomad NFE
AF:
0.221
Gnomad OTH
AF:
0.306
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.304
AC:
46190
AN:
151836
Hom.:
8446
Cov.:
31
AF XY:
0.301
AC XY:
22331
AN XY:
74200
show subpopulations
African (AFR)
AF:
0.522
AC:
21598
AN:
41358
American (AMR)
AF:
0.202
AC:
3088
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.276
AC:
956
AN:
3462
East Asian (EAS)
AF:
0.183
AC:
943
AN:
5146
South Asian (SAS)
AF:
0.216
AC:
1038
AN:
4812
European-Finnish (FIN)
AF:
0.248
AC:
2613
AN:
10530
Middle Eastern (MID)
AF:
0.286
AC:
84
AN:
294
European-Non Finnish (NFE)
AF:
0.221
AC:
15003
AN:
67958
Other (OTH)
AF:
0.305
AC:
644
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1493
2986
4480
5973
7466
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
442
884
1326
1768
2210
<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:
0.223
Hom.:
4594
Bravo
AF:
0.312
Asia WGS
AF:
0.211
AC:
732
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
4.7
DANN
Benign
0.78
PhyloP100
0.16
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs2609224; hg19: chr7-34706406; API