chr11-89449498-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_016931.5(NOX4):c.291G>T(p.Leu97Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0032 in 1,611,924 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0033 ( 14 hom. )
Consequence
NOX4
NM_016931.5 missense
NM_016931.5 missense
Scores
7
10
Clinical Significance
Conservation
PhyloP100: 0.241
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 -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.05311069).
BP6
?
Variant 11-89449498-C-A is Benign according to our data. Variant chr11-89449498-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 707952.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOX4 | NM_016931.5 | c.291G>T | p.Leu97Phe | missense_variant | 4/18 | ENST00000263317.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOX4 | ENST00000263317.9 | c.291G>T | p.Leu97Phe | missense_variant | 4/18 | 1 | NM_016931.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00202 AC: 308AN: 152118Hom.: 0 Cov.: 32
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152118
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GnomAD3 exomes AF: 0.00153 AC: 379AN: 247798Hom.: 1 AF XY: 0.00151 AC XY: 203AN XY: 134154
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GnomAD4 exome AF: 0.00332 AC: 4850AN: 1459688Hom.: 14 Cov.: 29 AF XY: 0.00320 AC XY: 2324AN XY: 726214
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GnomAD4 genome ? AF: 0.00202 AC: 308AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.00168 AC XY: 125AN XY: 74448
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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 | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;.;D;D;D;D;.;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D;D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;N;D;N;N;D;N;N
REVEL
Uncertain
Sift
Benign
T;T;T;T;T;T;T;T
Sift4G
Benign
T;T;T;D;T;T;T;T
Polyphen
0.028, 0.92, 0.13, 0.91
.;.;B;P;B;.;.;P
Vest4
MutPred
0.63
.;.;Gain of sheet (P = 0.039);Gain of sheet (P = 0.039);Gain of sheet (P = 0.039);.;.;.;
MVP
MPC
0.17
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at