chr12-117285808-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000620.5(NOS1):c.1290+296T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,146 control chromosomes in the GnomAD database, including 51,515 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 0.82 ( 51515 hom., cov: 32)
Consequence
NOS1
NM_000620.5 intron
NM_000620.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.140
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOS1 | NM_000620.5 | c.1290+296T>C | intron_variant | ENST00000317775.11 | |||
NOS1 | NM_001204213.2 | c.282+296T>C | intron_variant | ||||
NOS1 | NM_001204214.2 | c.282+296T>C | intron_variant | ||||
NOS1 | NM_001204218.2 | c.1290+296T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOS1 | ENST00000317775.11 | c.1290+296T>C | intron_variant | 1 | NM_000620.5 | P1 | |||
NOS1 | ENST00000338101.8 | c.1290+296T>C | intron_variant | 5 | |||||
NOS1 | ENST00000618760.4 | c.1290+296T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.822 AC: 124994AN: 152030Hom.: 51473 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.822 AC: 125091AN: 152146Hom.: 51515 Cov.: 32 AF XY: 0.821 AC XY: 61047AN XY: 74354
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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