7-151009827-G-A

Variant names:

• chr7-151009827-G-A
• rs743506
• NM_000603.5:c.2512+242G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000297494.8(NOS3):​c.2512+242G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,124 control chromosomes in the GnomAD database, including 39,020 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: 𝑓 0.71 (39020 hom., cov: 32)
• Consequence: NOS3 ENST00000297494.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 30 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000297494.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOS3	NM_000603.5	MANE Select	c.2512+242G>A		intron	N/A	NP_000594.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOS3	ENST00000297494.8	TSL:1 MANE Select	c.2512+242G>A		intron	N/A	ENSP00000297494.3
	NOS3	ENST00000461406.5	TSL:2	c.1894+242G>A		intron	N/A	ENSP00000417143.1
	NOS3	ENST00000475017.1	TSL:2	c.391+242G>A		intron	N/A	ENSP00000418245.1

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107615 AN: 152006 Hom.: 38995 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.706

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.708 AC: 107688 AN: 152124 Hom.: 39020 Cov.: 32 AF XY: 0.714 AC XY: 53072 AN XY: 74368

African (AFR) AF: 0.555 AC: 22989 AN: 41452

American (AMR) AF: 0.759 AC: 11618 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2541 AN: 3472

East Asian (EAS) AF: 0.785 AC: 4050 AN: 5156

South Asian (SAS) AF: 0.827 AC: 3987 AN: 4822

European-Finnish (FIN) AF: 0.834 AC: 8854 AN: 10610

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51170 AN: 67990

Other (OTH) AF: 0.708 AC: 1497 AN: 2114

Alfa AF: 0.734 Hom.: 52218

Bravo AF: 0.696

Asia WGS AF: 0.809 AC: 2810 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.28
PhyloP100		0.0090
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs743506; hg19: chr7-150706915; COSMIC: COSV52487605; COSMIC: COSV52487605;