7-151002383-AACACACACACACACACACACACACACACACACACACACACACACAC-AACACACACACACACACACACACACACACACACACACACACACAC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_000603.5(NOS3):c.1752+148_1752+149delAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 270,808 control chromosomes in the GnomAD database, including 95 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.045 ( 95 hom., cov: 0)
Exomes 𝑓: 0.0015 ( 0 hom. )
Consequence
NOS3
NM_000603.5 intron
NM_000603.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.222
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0634 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOS3 | NM_000603.5 | c.1752+148_1752+149delAC | intron_variant | ENST00000297494.8 | NP_000594.2 | |||
NOS3 | NM_001160111.1 | c.1752+148_1752+149delAC | intron_variant | NP_001153583.1 | ||||
NOS3 | NM_001160110.1 | c.1752+148_1752+149delAC | intron_variant | NP_001153582.1 | ||||
NOS3 | NM_001160109.2 | c.1752+148_1752+149delAC | intron_variant | NP_001153581.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0452 AC: 2940AN: 65038Hom.: 95 Cov.: 0
GnomAD3 genomes
AF:
AC:
2940
AN:
65038
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00153 AC: 314AN: 205714Hom.: 0 AF XY: 0.00160 AC XY: 182AN XY: 113892
GnomAD4 exome
AF:
AC:
314
AN:
205714
Hom.:
AF XY:
AC XY:
182
AN XY:
113892
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0452 AC: 2941AN: 65094Hom.: 95 Cov.: 0 AF XY: 0.0447 AC XY: 1341AN XY: 30006
GnomAD4 genome
AF:
AC:
2941
AN:
65094
Hom.:
Cov.:
0
AF XY:
AC XY:
1341
AN XY:
30006
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at