rs689453

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

Scores

2

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.183
Variant links:
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]

Genome browser will be placed here

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
NQO1NM_000903.3 linkuse as main transcriptc.72G>A p.Glu24Glu synonymous_variant 2/6 ENST00000320623.10 NP_000894.1 P15559-1
NQO1NM_001025433.2 linkuse as main transcriptc.72G>A p.Glu24Glu synonymous_variant 2/5 NP_001020604.1 P15559-2
NQO1NM_001025434.2 linkuse as main transcriptc.72G>A p.Glu24Glu synonymous_variant 2/5 NP_001020605.1 P15559-3
NQO1NM_001286137.2 linkuse as main transcriptc.72G>A p.Glu24Glu synonymous_variant 2/4 NP_001273066.1 B4DLR8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NQO1ENST00000320623.10 linkuse as main transcriptc.72G>A p.Glu24Glu synonymous_variant 2/61 NM_000903.3 ENSP00000319788.5 P15559-1

Frequencies

GnomAD3 genomes
AF:
0.0624
AC:
9497
AN:
152144
Hom.:
327
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0506
Gnomad AMI
AF:
0.114
Gnomad AMR
AF:
0.0523
Gnomad ASJ
AF:
0.0755
Gnomad EAS
AF:
0.000770
Gnomad SAS
AF:
0.0267
Gnomad FIN
AF:
0.0694
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.0763
Gnomad OTH
AF:
0.0664
GnomAD3 exomes
AF:
0.0584
AC:
14668
AN:
251314
Hom.:
527
AF XY:
0.0584
AC XY:
7929
AN XY:
135852
show subpopulations
Gnomad AFR exome
AF:
0.0472
Gnomad AMR exome
AF:
0.0369
Gnomad ASJ exome
AF:
0.0709
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0312
Gnomad FIN exome
AF:
0.0712
Gnomad NFE exome
AF:
0.0793
Gnomad OTH exome
AF:
0.0662
GnomAD4 exome
AF:
0.0710
AC:
103772
AN:
1461836
Hom.:
4083
Cov.:
31
AF XY:
0.0695
AC XY:
50559
AN XY:
727210
show subpopulations
Gnomad4 AFR exome
AF:
0.0518
Gnomad4 AMR exome
AF:
0.0394
Gnomad4 ASJ exome
AF:
0.0756
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0305
Gnomad4 FIN exome
AF:
0.0716
Gnomad4 NFE exome
AF:
0.0784
Gnomad4 OTH exome
AF:
0.0679
GnomAD4 genome
AF:
0.0625
AC:
9515
AN:
152262
Hom.:
330
Cov.:
32
AF XY:
0.0609
AC XY:
4532
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.0510
Gnomad4 AMR
AF:
0.0521
Gnomad4 ASJ
AF:
0.0755
Gnomad4 EAS
AF:
0.000771
Gnomad4 SAS
AF:
0.0265
Gnomad4 FIN
AF:
0.0694
Gnomad4 NFE
AF:
0.0763
Gnomad4 OTH
AF:
0.0662
Alfa
AF:
0.0742
Hom.:
827
Bravo
AF:
0.0626
Asia WGS
AF:
0.0200
AC:
70
AN:
3478
EpiCase
AF:
0.0815
EpiControl
AF:
0.0808

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 providedclinical testingPreventionGenetics, part of Exact SciencesOct 21, 2019This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.34
CADD
Benign
9.6
DANN
Benign
0.55

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs689453; hg19: chr16-69752373; COSMIC: COSV57731156; API