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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.908
Variant links:
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 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
NOS3NM_000603.5 linkc.1752+116_1752+149delACACACACACACACACACACACACACACACACAC intron_variant ENST00000297494.8 NP_000594.2 P29474-1
NOS3NM_001160111.1 linkc.1752+116_1752+149delACACACACACACACACACACACACACACACACAC intron_variant NP_001153583.1 P29474-2
NOS3NM_001160110.1 linkc.1752+116_1752+149delACACACACACACACACACACACACACACACACAC intron_variant NP_001153582.1 P29474-3
NOS3NM_001160109.2 linkc.1752+116_1752+149delACACACACACACACACACACACACACACACACAC intron_variant NP_001153581.1 P29474A0S0A6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NOS3ENST00000297494.8 linkc.1752+80_1752+113delACACACACACACACACACACACACACACACACAC intron_variant 1 NM_000603.5 ENSP00000297494.3 P29474-1

Frequencies

GnomAD3 genomes
AF:
0.00173
AC:
113
AN:
65212
Hom.:
1
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00584
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00126
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000627
Gnomad OTH
AF:
0.00117
GnomAD4 exome
AF:
0.000364
AC:
75
AN:
205818
Hom.:
0
AF XY:
0.000290
AC XY:
33
AN XY:
113950
show subpopulations
Gnomad4 AFR exome
AF:
0.00703
Gnomad4 AMR exome
AF:
0.000421
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000267
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000848
Gnomad4 OTH exome
AF:
0.000789
GnomAD4 genome
AF:
0.00175
AC:
114
AN:
65270
Hom.:
1
Cov.:
0
AF XY:
0.00170
AC XY:
51
AN XY:
30074
show subpopulations
Gnomad4 AFR
AF:
0.00582
Gnomad4 AMR
AF:
0.00143
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000627
Gnomad4 OTH
AF:
0.00115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3138808; hg19: chr7-150699471; API