chr11-89402500-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_016931.5(NOX4):c.672C>T(p.Pro224=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,611,256 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00089 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 1 hom. )
Consequence
NOX4
NM_016931.5 synonymous
NM_016931.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0290
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 11-89402500-G-A is Benign according to our data. Variant chr11-89402500-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 722792.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.029 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOX4 | NM_016931.5 | c.672C>T | p.Pro224= | synonymous_variant | 9/18 | ENST00000263317.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOX4 | ENST00000263317.9 | c.672C>T | p.Pro224= | synonymous_variant | 9/18 | 1 | NM_016931.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000894 AC: 136AN: 152052Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000804 AC: 199AN: 247422Hom.: 1 AF XY: 0.000814 AC XY: 109AN XY: 133888
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GnomAD4 exome AF: 0.00121 AC: 1762AN: 1459086Hom.: 1 Cov.: 31 AF XY: 0.00126 AC XY: 912AN XY: 725812
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GnomAD4 genome ? AF: 0.000894 AC: 136AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.000672 AC XY: 50AN XY: 74372
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 06, 2018 | - - |
Computational scores
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Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at