rs3730006
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000603.5(NOS3):c.2245+27G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 1,612,764 control chromosomes in the GnomAD database, including 461 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 0.021 ( 33 hom., cov: 33)
Exomes 𝑓: 0.022 ( 428 hom. )
Consequence
NOS3
NM_000603.5 intron
NM_000603.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.708
Genes affected
NOS3 (HGNC:7876): (nitric oxide synthase 3) Nitric oxide is a reactive free radical which acts as a biologic mediator in several processes, including neurotransmission and antimicrobial and antitumoral activities. Nitric oxide is synthesized from L-arginine by nitric oxide synthases. Variations in this gene are associated with susceptibility to coronary spasm. Alternative splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Oct 2016]
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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=-0.88).
BA1
?
GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.055 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOS3 | NM_000603.5 | c.2245+27G>A | intron_variant | ENST00000297494.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOS3 | ENST00000297494.8 | c.2245+27G>A | intron_variant | 1 | NM_000603.5 | P1 | |||
NOS3 | ENST00000461406.5 | c.1627+27G>A | intron_variant | 2 | |||||
NOS3 | ENST00000475017.1 | c.126+27G>A | intron_variant | 2 | |||||
NOS3 | ENST00000473057.1 | n.189+27G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0207 AC: 3148AN: 152116Hom.: 33 Cov.: 33
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GnomAD3 exomes AF: 0.0187 AC: 4623AN: 246770Hom.: 71 AF XY: 0.0189 AC XY: 2526AN XY: 133942
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GnomAD4 exome AF: 0.0216 AC: 31617AN: 1460530Hom.: 428 Cov.: 32 AF XY: 0.0215 AC XY: 15633AN XY: 726538
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GnomAD4 genome ? AF: 0.0207 AC: 3152AN: 152234Hom.: 33 Cov.: 33 AF XY: 0.0197 AC XY: 1470AN XY: 74440
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at