7-151002383-AACACACACACACACACACACACACACACACACACACACACACACAC-AACACACACACACAC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_000603.5(NOS3):c.1752+118_1752+149delACACACACACACACACACACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00439 in 271,048 control chromosomes in the GnomAD database, including 26 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.015 ( 23 hom., cov: 0)
Exomes 𝑓: 0.0010 ( 3 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 Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.015 (981/65262) while in subpopulation AFR AF= 0.0519 (918/17680). AF 95% confidence interval is 0.0491. There are 23 homozygotes in gnomad4. There are 495 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 981 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOS3 | NM_000603.5 | c.1752+118_1752+149delACACACACACACACACACACACACACACACAC | intron_variant | ENST00000297494.8 | NP_000594.2 | |||
NOS3 | NM_001160111.1 | c.1752+118_1752+149delACACACACACACACACACACACACACACACAC | intron_variant | NP_001153583.1 | ||||
NOS3 | NM_001160110.1 | c.1752+118_1752+149delACACACACACACACACACACACACACACACAC | intron_variant | NP_001153582.1 | ||||
NOS3 | NM_001160109.2 | c.1752+118_1752+149delACACACACACACACACACACACACACACACAC | intron_variant | NP_001153581.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0151 AC: 985AN: 65204Hom.: 23 Cov.: 0
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GnomAD4 exome AF: 0.00102 AC: 209AN: 205786Hom.: 3 AF XY: 0.000851 AC XY: 97AN XY: 113938
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GnomAD4 genome AF: 0.0150 AC: 981AN: 65262Hom.: 23 Cov.: 0 AF XY: 0.0165 AC XY: 495AN XY: 30070
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at