rs6505469

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000625.4(NOS2):​c.468-1754A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,038 control chromosomes in the GnomAD database, including 30,225 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 0.62 ( 30225 hom., cov: 32)

Consequence

NOS2
NM_000625.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0160
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NOS2NM_000625.4 linkuse as main transcriptc.468-1754A>T intron_variant ENST00000313735.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NOS2ENST00000313735.11 linkuse as main transcriptc.468-1754A>T intron_variant 1 NM_000625.4 P2P35228-1

Frequencies

GnomAD3 genomes
AF:
0.619
AC:
94017
AN:
151920
Hom.:
30161
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.795
Gnomad AMI
AF:
0.650
Gnomad AMR
AF:
0.622
Gnomad ASJ
AF:
0.608
Gnomad EAS
AF:
0.398
Gnomad SAS
AF:
0.689
Gnomad FIN
AF:
0.554
Gnomad MID
AF:
0.639
Gnomad NFE
AF:
0.533
Gnomad OTH
AF:
0.604
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.619
AC:
94148
AN:
152038
Hom.:
30225
Cov.:
32
AF XY:
0.622
AC XY:
46229
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.795
Gnomad4 AMR
AF:
0.622
Gnomad4 ASJ
AF:
0.608
Gnomad4 EAS
AF:
0.398
Gnomad4 SAS
AF:
0.690
Gnomad4 FIN
AF:
0.554
Gnomad4 NFE
AF:
0.534
Gnomad4 OTH
AF:
0.606
Alfa
AF:
0.571
Hom.:
3047
Bravo
AF:
0.629
Asia WGS
AF:
0.561
AC:
1955
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.9
DANN
Benign
0.58

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6505469; hg19: chr17-26111886; API