12-117350435-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000620.5(NOS1):c.-421+11077G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,128 control chromosomes in the GnomAD database, including 2,795 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 0.17 (2795 hom., cov: 32)
• Consequence: NOS1 NM_000620.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOS1	NM_000620.5	c.-421+11077G>A		intron_variant		ENST00000317775.11
NOS1	NM_001204218.2	c.-421+11077G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOS1	ENST00000317775.11	c.-421+11077G>A		intron_variant		1	NM_000620.5	P1
NOS1	ENST00000618760.4	c.-421+11077G>A		intron_variant		5
NOS1	ENST00000477584.1	n.119-2043G>A		intron_variant, non_coding_transcript_variant		2
NOS1	ENST00000549189.1	n.471-18946G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26246 AN: 152008 Hom.: 2796 Cov.: 32

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.172 AC: 26239 AN: 152128 Hom.: 2795 Cov.: 32 AF XY: 0.177 AC XY: 13181 AN XY: 74362

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.174

Alfa AF: 0.182 Hom.: 602

Bravo AF: 0.162

Asia WGS AF: 0.229 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	4.6
Dann	Benign	0.78

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: rs3782219; hg19: chr12-117788240;