12-117348300-A-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000620.5(NOS1):c.-421+13212T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 31)
Failed GnomAD Quality Control
Consequence
NOS1
NM_000620.5 intron
NM_000620.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0760
Publications
13 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: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000620.5. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NOS1 | TSL:1 MANE Select | c.-421+13212T>A | intron | N/A | ENSP00000320758.6 | P29475-1 | |||
| NOS1 | TSL:5 | c.-421+13212T>A | intron | N/A | ENSP00000477999.1 | P29475-5 | |||
| NOS1 | TSL:2 | n.211T>A | non_coding_transcript_exon | Exon 2 of 2 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151918Hom.: 0 Cov.: 31
GnomAD3 genomes
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151918
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31
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GnomAD4 exome Cov.: 0
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GnomAD4 genome 0.00 AC: 0AN: 151918Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74188
GnomAD4 genome
Data not reliable, filtered out with message: AC0
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151918
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31
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74188
African (AFR)
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41344
American (AMR)
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15256
Ashkenazi Jewish (ASJ)
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3470
East Asian (EAS)
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5170
South Asian (SAS)
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4822
European-Finnish (FIN)
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10562
Middle Eastern (MID)
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316
European-Non Finnish (NFE)
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67980
Other (OTH)
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2090
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
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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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