Genetic Variant NOS3:c.1752+108_1752+149delACACACACACACACACACACACACACACACACACACACACAC (chr7-151002383-AACACACACACACACACACACACACACACACACACACACACAC-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_000603.5(NOS3):c.1752+108_1752+149delACACACACACACACACACACACACACACACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000486 in 205,824 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 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0000049 ( 0 hom. )

Failed GnomAD Quality Control

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]

NOS3 links:

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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	Effect	Exon rank	MANE	Protein	UniProt
NOS3	NM_000603.5 link	c.1752+108_1752+149delACACACACACACACACACACACACACACACACACACACACAC	intron_variant	Intron 14 of 26	ENST00000297494.8	NP_000594.2	P29474-1
NOS3	NM_001160111.1 link	c.1752+108_1752+149delACACACACACACACACACACACACACACACACACACACACAC	intron_variant	Intron 13 of 13		NP_001153583.1	P29474-2
NOS3	NM_001160110.1 link	c.1752+108_1752+149delACACACACACACACACACACACACACACACACACACACACAC	intron_variant	Intron 13 of 13		NP_001153582.1	P29474-3
NOS3	NM_001160109.2 link	c.1752+108_1752+149delACACACACACACACACACACACACACACACACACACACACAC	intron_variant	Intron 13 of 13		NP_001153581.1	P29474A0S0A6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOS3	ENST00000297494.8 link	c.1752+80_1752+121delACACACACACACACACACACACACACACACACACACACACAC		intron_variant	Intron 14 of 26	1	NM_000603.5	ENSP00000297494.3		P29474-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

65212

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

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:

0.00000486

AC:

AN:

205824

Hom.:

AF XY:

0.00

AC XY:

AN XY:

113952

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

6834

American (AMR)

AF:

0.00

AC:

AN:

19016

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6864

East Asian (EAS)

AF:

0.00

AC:

AN:

7492

South Asian (SAS)

AF:

0.00

AC:

AN:

38614

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9822

Middle Eastern (MID)

AF:

0.00

AC:

AN:

842

European-Non Finnish (NFE)

AF:

0.00000942

AC:

AN:

106196

Other (OTH)

AF:

0.00

AC:

AN:

10144

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

65212

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

30002

African (AFR)

AF:

0.00

AC:

AN:

17620

American (AMR)

AF:

0.00

AC:

AN:

5574

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2006

East Asian (EAS)

AF:

0.00

AC:

AN:

2316

South Asian (SAS)

AF:

0.00

AC:

AN:

1580

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2778

Middle Eastern (MID)

AF:

0.00

AC:

AN:

140

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

31906

Other (OTH)

AF:

0.00

AC:

AN:

858

Alfa

AF:

0.00

Hom.:

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

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7-151002383-AACACACACACACACACACACACACACACACACACACACACACACAC-AACAC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over