NM_000625.4:c.2800+450T>C

Variant names:

• chr17-27762348-A-G
• rs9906835
• NM_000625.4:c.2800+450T>C

Variant summary

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

The NM_000625.4(NOS2):​c.2800+450T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,074 control chromosomes in the GnomAD database, including 13,591 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 0.42 (13591 hom., cov: 32)
• Consequence: NOS2 NM_000625.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 19 publications found

Genes affected

NOS2 (HGNC:7873): (nitric oxide synthase 2) Nitric oxide is a reactive free radical which acts as a biologic mediator in several processes, including neurotransmission and antimicrobial and antitumoral activities. This gene encodes a nitric oxide synthase which is expressed in liver and is inducible by a combination of lipopolysaccharide and certain cytokines. Three related pseudogenes are located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]

NOS2 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOS2	NM_000625.4	c.2800+450T>C		intron_variant	Intron 22 of 26	ENST00000313735.11	NP_000616.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOS2	ENST00000313735.11	c.2800+450T>C		intron_variant	Intron 22 of 26	1	NM_000625.4	ENSP00000327251.6

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63814 AN: 151956 Hom.: 13567 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.420 AC: 63878 AN: 152074 Hom.: 13591 Cov.: 32 AF XY: 0.421 AC XY: 31304 AN XY: 74318

African (AFR) AF: 0.428 AC: 17750 AN: 41476

American (AMR) AF: 0.461 AC: 7050 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1352 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1824 AN: 5164

South Asian (SAS) AF: 0.586 AC: 2820 AN: 4814

European-Finnish (FIN) AF: 0.373 AC: 3951 AN: 10582

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27791 AN: 67972

Other (OTH) AF: 0.430 AC: 908 AN: 2112

Alfa AF: 0.411 Hom.: 3620

Bravo AF: 0.420

Asia WGS AF: 0.469 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.58
DANN	Benign	0.66
PhyloP100		0.21
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: rs9906835; hg19: chr17-26089374;