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

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 315 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NOS3NM_000603.5 linkc.1752+122_1752+149delACACACACACACACACACACACACACAC intron_variant ENST00000297494.8 NP_000594.2 P29474-1
NOS3NM_001160111.1 linkc.1752+122_1752+149delACACACACACACACACACACACACACAC intron_variant NP_001153583.1 P29474-2
NOS3NM_001160110.1 linkc.1752+122_1752+149delACACACACACACACACACACACACACAC intron_variant NP_001153582.1 P29474-3
NOS3NM_001160109.2 linkc.1752+122_1752+149delACACACACACACACACACACACACACAC 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+107delACACACACACACACACACACACACACAC intron_variant 1 NM_000603.5 ENSP00000297494.3 P29474-1

Frequencies

GnomAD3 genomes
AF:
0.00474
AC:
309
AN:
65214
Hom.:
2
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00721
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00484
Gnomad ASJ
AF:
0.000499
Gnomad EAS
AF:
0.00173
Gnomad SAS
AF:
0.00190
Gnomad FIN
AF:
0.00828
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00382
Gnomad OTH
AF:
0.00233
GnomAD4 exome
AF:
0.00286
AC:
589
AN:
205676
Hom.:
2
AF XY:
0.00283
AC XY:
322
AN XY:
113860
show subpopulations
Gnomad4 AFR exome
AF:
0.00483
Gnomad4 AMR exome
AF:
0.00100
Gnomad4 ASJ exome
AF:
0.00277
Gnomad4 EAS exome
AF:
0.00468
Gnomad4 SAS exome
AF:
0.00360
Gnomad4 FIN exome
AF:
0.00316
Gnomad4 NFE exome
AF:
0.00270
Gnomad4 OTH exome
AF:
0.00237
GnomAD4 genome
AF:
0.00483
AC:
315
AN:
65272
Hom.:
2
Cov.:
0
AF XY:
0.00509
AC XY:
153
AN XY:
30076
show subpopulations
Gnomad4 AFR
AF:
0.00746
Gnomad4 AMR
AF:
0.00484
Gnomad4 ASJ
AF:
0.000499
Gnomad4 EAS
AF:
0.00173
Gnomad4 SAS
AF:
0.00192
Gnomad4 FIN
AF:
0.00828
Gnomad4 NFE
AF:
0.00386
Gnomad4 OTH
AF:
0.00230

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