chr7-34666794-A-C
Variant names:
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
NM_207172.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.162
Publications
5 publications found
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 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 |
---|---|---|---|---|---|---|---|---|
NPSR1 | NM_207172.2 | c.147+8235A>C | intron_variant | Intron 1 of 8 | ENST00000360581.6 | NP_997055.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.304 AC: 46129AN: 151718Hom.: 8434 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
46129
AN:
151718
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.304 AC: 46190AN: 151836Hom.: 8446 Cov.: 31 AF XY: 0.301 AC XY: 22331AN XY: 74200 show subpopulations
GnomAD4 genome
AF:
AC:
46190
AN:
151836
Hom.:
Cov.:
31
AF XY:
AC XY:
22331
AN XY:
74200
show subpopulations
African (AFR)
AF:
AC:
21598
AN:
41358
American (AMR)
AF:
AC:
3088
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
AC:
956
AN:
3462
East Asian (EAS)
AF:
AC:
943
AN:
5146
South Asian (SAS)
AF:
AC:
1038
AN:
4812
European-Finnish (FIN)
AF:
AC:
2613
AN:
10530
Middle Eastern (MID)
AF:
AC:
84
AN:
294
European-Non Finnish (NFE)
AF:
AC:
15003
AN:
67958
Other (OTH)
AF:
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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
732
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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