rs9658354

Variant names:

• chr12-117286420-A-T
• rs9658354
• NM_000620.5:c.1128-154T>A

Variant summary

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

The NM_000620.5(NOS1):​c.1128-154T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,080 control chromosomes in the GnomAD database, including 13,031 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (13031 hom., cov: 32)
• Consequence: NOS1 NM_000620.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

Genes affected

NOS1 (HGNC:7872): (nitric oxide synthase 1) The protein encoded by this gene belongs to the family of nitric oxide synthases, which synthesize nitric oxide from L-arginine. Nitric oxide is a reactive free radical, which acts as a biologic mediator in several processes, including neurotransmission, and antimicrobial and antitumoral activities. In the brain and peripheral nervous system, nitric oxide displays many properties of a neurotransmitter, and has been implicated in neurotoxicity associated with stroke and neurodegenerative diseases, neural regulation of smooth muscle, including peristalsis, and penile erection. This protein is ubiquitously expressed, with high level of expression in skeletal muscle. Multiple transcript variants that differ in the 5' UTR have been described for this gene but the full-length nature of these transcripts is not known. Additionally, alternatively spliced transcript variants encoding different isoforms (some testis-specific) have been found for this gene.[provided by RefSeq, Feb 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOS1	NM_000620.5	c.1128-154T>A		intron_variant	Intron 5 of 28	ENST00000317775.11	NP_000611.1
NOS1	NM_001204218.2	c.1128-154T>A		intron_variant	Intron 5 of 29		NP_001191147.1
NOS1	NM_001204213.2	c.120-154T>A		intron_variant	Intron 4 of 27		NP_001191142.1
NOS1	NM_001204214.2	c.120-154T>A		intron_variant	Intron 4 of 27		NP_001191143.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOS1	ENST00000317775.11	c.1128-154T>A		intron_variant	Intron 5 of 28	1	NM_000620.5	ENSP00000320758.6
NOS1	ENST00000338101.8	c.1128-154T>A		intron_variant	Intron 4 of 28	5		ENSP00000337459.4
NOS1	ENST00000618760.4	c.1128-154T>A		intron_variant	Intron 5 of 29	5		ENSP00000477999.1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61911 AN: 151964 Hom.: 13019 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.407 AC: 61963 AN: 152080 Hom.: 13031 Cov.: 32 AF XY: 0.408 AC XY: 30347 AN XY: 74354

Gnomad4 AFR AF: 0.326 AC: 0.326052 AN: 0.326052

Gnomad4 AMR AF: 0.509 AC: 0.508516 AN: 0.508516

Gnomad4 ASJ AF: 0.458 AC: 0.458189 AN: 0.458189

Gnomad4 EAS AF: 0.409 AC: 0.409389 AN: 0.409389

Gnomad4 SAS AF: 0.490 AC: 0.489614 AN: 0.489614

Gnomad4 FIN AF: 0.396 AC: 0.395975 AN: 0.395975

Gnomad4 NFE AF: 0.429 AC: 0.428756 AN: 0.428756

Gnomad4 OTH AF: 0.417 AC: 0.417062 AN: 0.417062

Alfa AF: 0.414 Hom.: 1646

Bravo AF: 0.413

Asia WGS AF: 0.429 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.46
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

Publications

LitVar

Other links and lift over

dbSNP: rs9658354; hg19: chr12-117724225;