7-151002383-AACACACACACACACACACACACACACACACACACACACACACACAC-AACACACACACAC
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000603.5(NOS3):c.1752+116_1752+149delACACACACACACACACACACACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000697 in 271,088 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0017 ( 1 hom., cov: 0)
Exomes 𝑓: 0.00036 ( 0 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 114 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOS3 | NM_000603.5 | c.1752+116_1752+149delACACACACACACACACACACACACACACACACAC | intron_variant | ENST00000297494.8 | NP_000594.2 | |||
NOS3 | NM_001160111.1 | c.1752+116_1752+149delACACACACACACACACACACACACACACACACAC | intron_variant | NP_001153583.1 | ||||
NOS3 | NM_001160110.1 | c.1752+116_1752+149delACACACACACACACACACACACACACACACACAC | intron_variant | NP_001153582.1 | ||||
NOS3 | NM_001160109.2 | c.1752+116_1752+149delACACACACACACACACACACACACACACACACAC | intron_variant | NP_001153581.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00173 AC: 113AN: 65212Hom.: 1 Cov.: 0
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GnomAD4 exome AF: 0.000364 AC: 75AN: 205818Hom.: 0 AF XY: 0.000290 AC XY: 33AN XY: 113950
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GnomAD4 genome AF: 0.00175 AC: 114AN: 65270Hom.: 1 Cov.: 0 AF XY: 0.00170 AC XY: 51AN XY: 30074
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at