7-151002383-AACACACACACACACACACACACACACACACACACACACACACACAC-AACACACACACACACACAC
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000603.5(NOS3):c.1752+122_1752+149delACACACACACACACACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00334 in 270,948 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0048 ( 2 hom., cov: 0)
Exomes 𝑓: 0.0029 ( 2 hom. )
Consequence
NOS3
NM_000603.5 intron
NM_000603.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.908
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 Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 315 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOS3 | NM_000603.5 | c.1752+122_1752+149delACACACACACACACACACACACACACAC | intron_variant | ENST00000297494.8 | NP_000594.2 | |||
NOS3 | NM_001160111.1 | c.1752+122_1752+149delACACACACACACACACACACACACACAC | intron_variant | NP_001153583.1 | ||||
NOS3 | NM_001160110.1 | c.1752+122_1752+149delACACACACACACACACACACACACACAC | intron_variant | NP_001153582.1 | ||||
NOS3 | NM_001160109.2 | c.1752+122_1752+149delACACACACACACACACACACACACACAC | intron_variant | NP_001153581.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00474 AC: 309AN: 65214Hom.: 2 Cov.: 0
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GnomAD4 exome AF: 0.00286 AC: 589AN: 205676Hom.: 2 AF XY: 0.00283 AC XY: 322AN XY: 113860
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GnomAD4 genome AF: 0.00483 AC: 315AN: 65272Hom.: 2 Cov.: 0 AF XY: 0.00509 AC XY: 153AN XY: 30076
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at