rs28998802

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000625.4(NOS2):​c.110+818C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,102 control chromosomes in the GnomAD database, including 1,268 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 0.11 ( 1268 hom., cov: 32)

Consequence

NOS2
NM_000625.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.592
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NOS2NM_000625.4 linkc.110+818C>T intron_variant Intron 2 of 26 ENST00000313735.11 NP_000616.3 P35228-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NOS2ENST00000313735.11 linkc.110+818C>T intron_variant Intron 2 of 26 1 NM_000625.4 ENSP00000327251.6 P35228-1
NOS2ENST00000697337.1 linkn.110+818C>T intron_variant Intron 1 of 23 ENSP00000513259.1 A0A8V8TLB1

Frequencies

GnomAD3 genomes
AF:
0.112
AC:
16963
AN:
151984
Hom.:
1265
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0297
Gnomad AMI
AF:
0.101
Gnomad AMR
AF:
0.150
Gnomad ASJ
AF:
0.115
Gnomad EAS
AF:
0.0175
Gnomad SAS
AF:
0.184
Gnomad FIN
AF:
0.194
Gnomad MID
AF:
0.0791
Gnomad NFE
AF:
0.142
Gnomad OTH
AF:
0.110
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.112
AC:
16981
AN:
152102
Hom.:
1268
Cov.:
32
AF XY:
0.115
AC XY:
8548
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.0297
AC:
0.029681
AN:
0.029681
Gnomad4 AMR
AF:
0.149
AC:
0.149476
AN:
0.149476
Gnomad4 ASJ
AF:
0.115
AC:
0.115407
AN:
0.115407
Gnomad4 EAS
AF:
0.0174
AC:
0.0173879
AN:
0.0173879
Gnomad4 SAS
AF:
0.185
AC:
0.185116
AN:
0.185116
Gnomad4 FIN
AF:
0.194
AC:
0.19375
AN:
0.19375
Gnomad4 NFE
AF:
0.142
AC:
0.142412
AN:
0.142412
Gnomad4 OTH
AF:
0.114
AC:
0.113636
AN:
0.113636
Heterozygous variant carriers
0
743
1486
2228
2971
3714
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
188
376
564
752
940
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.101
Hom.:
264
Bravo
AF:
0.102
Asia WGS
AF:
0.122
AC:
425
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.77
DANN
Benign
0.57
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

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

Other links and lift over

dbSNP: rs28998802; hg19: chr17-26124908; API