chr11-89494453-G-A

Variant summary

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

The NM_001143837.2(NOX4):​c.-114-2234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,016 control chromosomes in the GnomAD database, including 34,078 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 0.65 ( 34078 hom., cov: 32)

Consequence

NOX4
NM_001143837.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0210
Variant links:
Genes affected
NOX4 (HGNC:7891): (NADPH oxidase 4) This gene encodes a member of the NOX-family of enzymes that functions as the catalytic subunit the NADPH oxidase complex. The encoded protein is localized to non-phagocytic cells where it acts as an oxygen sensor and catalyzes the reduction of molecular oxygen to various reactive oxygen species (ROS). The ROS generated by this protein have been implicated in numerous biological functions including signal transduction, cell differentiation and tumor cell growth. A pseudogene has been identified on the other arm of chromosome 11. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jan 2009]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NOX4NM_001143837.2 linkuse as main transcriptc.-114-2234C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NOX4ENST00000527956.5 linkuse as main transcriptc.-114-2234C>T intron_variant 5 Q9NPH5-8

Frequencies

GnomAD3 genomes
AF:
0.648
AC:
98419
AN:
151898
Hom.:
34071
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.416
Gnomad AMI
AF:
0.735
Gnomad AMR
AF:
0.598
Gnomad ASJ
AF:
0.722
Gnomad EAS
AF:
0.512
Gnomad SAS
AF:
0.648
Gnomad FIN
AF:
0.602
Gnomad MID
AF:
0.750
Gnomad NFE
AF:
0.811
Gnomad OTH
AF:
0.677
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.648
AC:
98467
AN:
152016
Hom.:
34078
Cov.:
32
AF XY:
0.637
AC XY:
47332
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.416
Gnomad4 AMR
AF:
0.597
Gnomad4 ASJ
AF:
0.722
Gnomad4 EAS
AF:
0.512
Gnomad4 SAS
AF:
0.650
Gnomad4 FIN
AF:
0.602
Gnomad4 NFE
AF:
0.811
Gnomad4 OTH
AF:
0.680
Alfa
AF:
0.762
Hom.:
17923
Bravo
AF:
0.632
Asia WGS
AF:
0.571
AC:
1985
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.6
DANN
Benign
0.56

Splicing

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: rs585197; hg19: chr11-89227621; API