rs36036826
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024505.4(NOX5):āc.290A>Gā(p.Lys97Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,388 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes š: 6.9e-7 ( 0 hom. )
Consequence
NOX5
NM_024505.4 missense
NM_024505.4 missense
Scores
7
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.74
Genes affected
NOX5 (HGNC:14874): (NADPH oxidase 5) This gene is predominantly expressed in the testis and lymphocyte-rich areas of spleen and lymph nodes. It encodes a calcium-dependen NADPH oxidase that generates superoxide, and functions as a calcium-dependent proton channel that may regulate redox-dependent processes in lymphocytes and spermatozoa. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOX5 | NM_024505.4 | c.290A>G | p.Lys97Arg | missense_variant | 3/16 | ENST00000388866.8 | NP_078781.3 | |
NOX5 | NM_001184779.2 | c.290A>G | p.Lys97Arg | missense_variant | 3/16 | NP_001171708.1 | ||
SPESP1-NOX5 | NM_001184780.2 | c.269A>G | p.Lys90Arg | missense_variant | 3/16 | NP_001171709.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248852Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134478
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GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459388Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 725988
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;.;.;T;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;.;M;M
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D;D;D
REVEL
Uncertain
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
0.98, 0.96, 0.98
.;.;D;D;D
Vest4
MutPred
0.44
.;.;.;Loss of ubiquitination at K97 (P = 0.0326);Loss of ubiquitination at K97 (P = 0.0326);
MVP
MPC
0.24
ClinPred
D
GERP RS
Varity_R
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