rs7929532

Variant summary

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

The NM_016931.5(NOX4):​c.630-3284T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0923 in 151,642 control chromosomes in the GnomAD database, including 783 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 0.092 ( 783 hom., cov: 31)

Consequence

NOX4
NM_016931.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.02
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NOX4NM_016931.5 linkuse as main transcriptc.630-3284T>C intron_variant ENST00000263317.9 NP_058627.2 Q9NPH5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NOX4ENST00000263317.9 linkuse as main transcriptc.630-3284T>C intron_variant 1 NM_016931.5 ENSP00000263317.4 Q9NPH5-1

Frequencies

GnomAD3 genomes
AF:
0.0924
AC:
13995
AN:
151540
Hom.:
785
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0798
Gnomad AMI
AF:
0.116
Gnomad AMR
AF:
0.148
Gnomad ASJ
AF:
0.0205
Gnomad EAS
AF:
0.166
Gnomad SAS
AF:
0.186
Gnomad FIN
AF:
0.144
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0719
Gnomad OTH
AF:
0.0635
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0923
AC:
14002
AN:
151642
Hom.:
783
Cov.:
31
AF XY:
0.0978
AC XY:
7242
AN XY:
74062
show subpopulations
Gnomad4 AFR
AF:
0.0798
Gnomad4 AMR
AF:
0.147
Gnomad4 ASJ
AF:
0.0205
Gnomad4 EAS
AF:
0.165
Gnomad4 SAS
AF:
0.187
Gnomad4 FIN
AF:
0.144
Gnomad4 NFE
AF:
0.0719
Gnomad4 OTH
AF:
0.0634
Alfa
AF:
0.0803
Hom.:
285
Bravo
AF:
0.0884
Asia WGS
AF:
0.131
AC:
456
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
3.3
DANN
Benign
0.75

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: rs7929532; hg19: chr11-89138994; API