rs4149360
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000904.6(NQO2):c.7+14A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,588,476 control chromosomes in the GnomAD database, including 34,947 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 0.16 ( 2436 hom., cov: 31)
Exomes 𝑓: 0.21 ( 32511 hom. )
Consequence
NQO2
NM_000904.6 intron
NM_000904.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.338
Genes affected
NQO2 (HGNC:7856): (N-ribosyldihydronicotinamide:quinone dehydrogenase 2) This gene encodes a member of the thioredoxin family of enzymes. It is a cytosolic and ubiquitously expressed flavoprotein that catalyzes the two-electron reduction of quinone substrates and uses dihydronicotinamide riboside as a reducing coenzyme. Mutations in this gene have been associated with neurodegenerative diseases and several cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NQO2 | NM_000904.6 | c.7+14A>G | intron_variant | ENST00000380455.11 | |||
NQO2 | NM_001290221.2 | c.7+14A>G | intron_variant | ||||
NQO2 | NM_001290222.2 | c.7+14A>G | intron_variant | ||||
NQO2 | NM_001318940.2 | c.7+14A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NQO2 | ENST00000380455.11 | c.7+14A>G | intron_variant | 1 | NM_000904.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.161 AC: 24340AN: 151554Hom.: 2435 Cov.: 31
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GnomAD3 exomes AF: 0.187 AC: 39489AN: 210714Hom.: 3890 AF XY: 0.187 AC XY: 21227AN XY: 113694
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GnomAD4 exome AF: 0.206 AC: 296168AN: 1436804Hom.: 32511 Cov.: 32 AF XY: 0.203 AC XY: 145082AN XY: 713480
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GnomAD4 genome ? AF: 0.161 AC: 24345AN: 151672Hom.: 2436 Cov.: 31 AF XY: 0.161 AC XY: 11953AN XY: 74100
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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