NM_000620.5:c.853-4108T>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_000620.5(NOS1):c.853-4108T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,060 control chromosomes in the GnomAD database, including 52,854 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 0.83 ( 52854 hom., cov: 31)
Consequence
NOS1
NM_000620.5 intron
NM_000620.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.788
Publications
18 publications found
Genes affected
NOS1 (HGNC:7872): (nitric oxide synthase 1) The protein encoded by this gene belongs to the family of nitric oxide synthases, which synthesize nitric oxide from L-arginine. Nitric oxide is a reactive free radical, which acts as a biologic mediator in several processes, including neurotransmission, and antimicrobial and antitumoral activities. In the brain and peripheral nervous system, nitric oxide displays many properties of a neurotransmitter, and has been implicated in neurotoxicity associated with stroke and neurodegenerative diseases, neural regulation of smooth muscle, including peristalsis, and penile erection. This protein is ubiquitously expressed, with high level of expression in skeletal muscle. Multiple transcript variants that differ in the 5' UTR have been described for this gene but the full-length nature of these transcripts is not known. Additionally, alternatively spliced transcript variants encoding different isoforms (some testis-specific) have been found for this gene.[provided by RefSeq, Feb 2011]
NOS1 Gene-Disease associations (from GenCC):
- idiopathic achalasiaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOS1 | NM_000620.5 | c.853-4108T>C | intron_variant | Intron 3 of 28 | ENST00000317775.11 | NP_000611.1 | ||
NOS1 | NM_001204218.2 | c.853-4108T>C | intron_variant | Intron 3 of 29 | NP_001191147.1 | |||
NOS1 | NM_001204213.2 | c.-156-4108T>C | intron_variant | Intron 2 of 27 | NP_001191142.1 | |||
NOS1 | NM_001204214.2 | c.-156-4108T>C | intron_variant | Intron 2 of 27 | NP_001191143.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOS1 | ENST00000317775.11 | c.853-4108T>C | intron_variant | Intron 3 of 28 | 1 | NM_000620.5 | ENSP00000320758.6 | |||
NOS1 | ENST00000338101.8 | c.853-4108T>C | intron_variant | Intron 2 of 28 | 5 | ENSP00000337459.4 | ||||
NOS1 | ENST00000618760.4 | c.853-4108T>C | intron_variant | Intron 3 of 29 | 5 | ENSP00000477999.1 |
Frequencies
GnomAD3 genomes AF: 0.833 AC: 126506AN: 151940Hom.: 52807 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
126506
AN:
151940
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: 0.833 AC: 126611AN: 152060Hom.: 52854 Cov.: 31 AF XY: 0.832 AC XY: 61813AN XY: 74314 show subpopulations
GnomAD4 genome
AF:
AC:
126611
AN:
152060
Hom.:
Cov.:
31
AF XY:
AC XY:
61813
AN XY:
74314
show subpopulations
African (AFR)
AF:
AC:
36236
AN:
41494
American (AMR)
AF:
AC:
12722
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
AC:
2943
AN:
3468
East Asian (EAS)
AF:
AC:
4128
AN:
5152
South Asian (SAS)
AF:
AC:
4088
AN:
4804
European-Finnish (FIN)
AF:
AC:
8463
AN:
10568
Middle Eastern (MID)
AF:
AC:
241
AN:
294
European-Non Finnish (NFE)
AF:
AC:
55318
AN:
68006
Other (OTH)
AF:
AC:
1738
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1080
2160
3241
4321
5401
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
884
1768
2652
3536
4420
<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:
2792
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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