GeneBe

rs3138808

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000603.5(NOS3):​c.1752+104_1752+149delACACACACACACACACACACACACACACACACACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000111 in 271,084 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000015 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000097 ( 0 hom. )

Consequence

NOS3
NM_000603.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.908

Publications

9 publications found
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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NOS3NM_000603.5 linkc.1752+104_1752+149delACACACACACACACACACACACACACACACACACACACACACACAC intron_variant Intron 14 of 26 ENST00000297494.8 NP_000594.2 P29474-1
NOS3NM_001160111.1 linkc.1752+104_1752+149delACACACACACACACACACACACACACACACACACACACACACACAC intron_variant Intron 13 of 13 NP_001153583.1 P29474-2
NOS3NM_001160110.1 linkc.1752+104_1752+149delACACACACACACACACACACACACACACACACACACACACACACAC intron_variant Intron 13 of 13 NP_001153582.1 P29474-3
NOS3NM_001160109.2 linkc.1752+104_1752+149delACACACACACACACACACACACACACACACACACACACACACACAC intron_variant Intron 13 of 13 NP_001153581.1 P29474A0S0A6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NOS3ENST00000297494.8 linkc.1752+80_1752+125delACACACACACACACACACACACACACACACACACACACACACACAC intron_variant Intron 14 of 26 1 NM_000603.5 ENSP00000297494.3 P29474-1

Frequencies

GnomAD3 genomes
AF:
0.0000153
AC:
1
AN:
65212
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000568
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000972
AC:
2
AN:
205814
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
113944
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
6834
American (AMR)
AF:
0.00
AC:
0
AN:
19016
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
6864
East Asian (EAS)
AF:
0.00
AC:
0
AN:
7492
South Asian (SAS)
AF:
0.0000518
AC:
2
AN:
38604
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9822
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
842
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
106196
Other (OTH)
AF:
0.00
AC:
0
AN:
10144
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.0000153
AC:
1
AN:
65270
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
30074
show subpopulations
African (AFR)
AF:
0.0000565
AC:
1
AN:
17688
American (AMR)
AF:
0.00
AC:
0
AN:
5584
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2006
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2310
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1566
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2778
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
132
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
31904
Other (OTH)
AF:
0.00
AC:
0
AN:
868
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.91

Splicing

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

Publications

Other links and lift over

dbSNP: rs3138808; hg19: chr7-150699471; API