rs689453
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1
The NM_000903.3(NQO1):c.72G>A(p.Glu24Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 1,614,098 control chromosomes in the GnomAD database, including 4,413 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.062 ( 330 hom., cov: 32)
Exomes 𝑓: 0.071 ( 4083 hom. )
Consequence
NQO1
NM_000903.3 synonymous
NM_000903.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.183
Genes affected
NQO1 (HGNC:2874): (NAD(P)H quinone dehydrogenase 1) This gene is a member of the NAD(P)H dehydrogenase (quinone) family and encodes a cytoplasmic 2-electron reductase. This FAD-binding protein forms homodimers and reduces quinones to hydroquinones. This protein's enzymatic activity prevents the one electron reduction of quinones that results in the production of radical species. Mutations in this gene have been associated with tardive dyskinesia (TD), an increased risk of hematotoxicity after exposure to benzene, and susceptibility to various forms of cancer. Altered expression of this protein has been seen in many tumors and is also associated with Alzheimer's disease (AD). Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 16-69718470-C-T is Benign according to our data. Variant chr16-69718470-C-T is described in ClinVar as [Benign]. Clinvar id is 3055562.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.183 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0746 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NQO1 | NM_000903.3 | c.72G>A | p.Glu24Glu | synonymous_variant | 2/6 | ENST00000320623.10 | NP_000894.1 | |
NQO1 | NM_001025433.2 | c.72G>A | p.Glu24Glu | synonymous_variant | 2/5 | NP_001020604.1 | ||
NQO1 | NM_001025434.2 | c.72G>A | p.Glu24Glu | synonymous_variant | 2/5 | NP_001020605.1 | ||
NQO1 | NM_001286137.2 | c.72G>A | p.Glu24Glu | synonymous_variant | 2/4 | NP_001273066.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NQO1 | ENST00000320623.10 | c.72G>A | p.Glu24Glu | synonymous_variant | 2/6 | 1 | NM_000903.3 | ENSP00000319788.5 |
Frequencies
GnomAD3 genomes AF: 0.0624 AC: 9497AN: 152144Hom.: 327 Cov.: 32
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GnomAD3 exomes AF: 0.0584 AC: 14668AN: 251314Hom.: 527 AF XY: 0.0584 AC XY: 7929AN XY: 135852
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GnomAD4 exome AF: 0.0710 AC: 103772AN: 1461836Hom.: 4083 Cov.: 31 AF XY: 0.0695 AC XY: 50559AN XY: 727210
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GnomAD4 genome AF: 0.0625 AC: 9515AN: 152262Hom.: 330 Cov.: 32 AF XY: 0.0609 AC XY: 4532AN XY: 74436
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
NQO1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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