Variant 7-151002383-AACACACACACACACACACACACACACACACACACACACACACACAC-AACACACACACACACACAC details in Genebe, Genetics Data Aggregator

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]

NOS3 links:

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	Effect	MANE	Protein	UniProt
NOS3	NM_000603.5 link	c.1752+122_1752+149delACACACACACACACACACACACACACAC	intron_variant	ENST00000297494.8	NP_000594.2	P29474-1
NOS3	NM_001160111.1 link	c.1752+122_1752+149delACACACACACACACACACACACACACAC	intron_variant		NP_001153583.1	P29474-2
NOS3	NM_001160110.1 link	c.1752+122_1752+149delACACACACACACACACACACACACACAC	intron_variant		NP_001153582.1	P29474-3
NOS3	NM_001160109.2 link	c.1752+122_1752+149delACACACACACACACACACACACACACAC	intron_variant		NP_001153581.1	P29474A0S0A6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NOS3	ENST00000297494.8 link	c.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.:

Cov.:

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.:

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.:

Cov.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over