15-69035485-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_024505.4(NOX5):c.987C>T(p.Thr329Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.934 in 1,614,026 control chromosomes in the GnomAD database, including 708,616 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 0.87 ( 58444 hom., cov: 32)
Exomes 𝑓: 0.94 ( 650172 hom. )
Consequence
NOX5
NM_024505.4 synonymous
NM_024505.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.27
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 Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP7
Synonymous conserved (PhyloP=-4.27 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOX5 | NM_024505.4 | c.987C>T | p.Thr329Thr | synonymous_variant | Exon 6 of 16 | ENST00000388866.8 | NP_078781.3 | |
NOX5 | NM_001184779.2 | c.903C>T | p.Thr301Thr | synonymous_variant | Exon 6 of 16 | NP_001171708.1 | ||
SPESP1-NOX5 | NM_001184780.2 | c.882C>T | p.Thr294Thr | synonymous_variant | Exon 6 of 16 | NP_001171709.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOX5 | ENST00000388866.8 | c.987C>T | p.Thr329Thr | synonymous_variant | Exon 6 of 16 | 1 | NM_024505.4 | ENSP00000373518.3 | ||
NOX5 | ENST00000260364.9 | c.933C>T | p.Thr311Thr | synonymous_variant | Exon 7 of 17 | 1 | ENSP00000454143.1 |
Frequencies
GnomAD3 genomes AF: 0.867 AC: 131783AN: 152076Hom.: 58423 Cov.: 32
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GnomAD3 exomes AF: 0.913 AC: 229047AN: 250988Hom.: 105540 AF XY: 0.917 AC XY: 124425AN XY: 135622
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GnomAD4 exome AF: 0.941 AC: 1375800AN: 1461832Hom.: 650172 Cov.: 57 AF XY: 0.941 AC XY: 684397AN XY: 727222
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GnomAD4 genome AF: 0.866 AC: 131845AN: 152194Hom.: 58444 Cov.: 32 AF XY: 0.867 AC XY: 64488AN XY: 74408
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at