Genetic Variant NQO1-DT:n.163+485C>T (chr16-69727660-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000575838.2(NQO1-DT):n.163+485C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,160 control chromosomes in the GnomAD database, including 57,261 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 ( 57261 hom., cov: 31)

Consequence

NQO1-DT
ENST00000575838.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.19

Publications

10 publications found

Variant links:

Genes affected

NQO1-DT (HGNC:55344): (NQO1 divergent transcript)

NQO1-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NQO1-DT	NR_186363.1 link	n.449+485C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NQO1-DT	ENST00000575838.2 link	n.163+485C>T	intron_variant	Intron 1 of 1	5
NQO1-DT	ENST00000690354.2 link	n.565+485C>T	intron_variant	Intron 1 of 1
NQO1-DT	ENST00000844536.1 link	n.445+485C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.866

AC:

131666

AN:

152042

Hom.:

57218

Cov.:

show subpopulations

Gnomad AFR

AF:

0.862

Gnomad AMI

AF:

0.880

Gnomad AMR

AF:

0.918

Gnomad ASJ

AF:

0.850

Gnomad EAS

AF:

0.640

Gnomad SAS

AF:

0.826

Gnomad FIN

AF:

0.855

Gnomad MID

AF:

0.861

Gnomad NFE

AF:

0.879

Gnomad OTH

AF:

0.868

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.866

AC:

131762

AN:

152160

Hom.:

57261

Cov.:

AF XY:

0.863

AC XY:

64194

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.862

AC:

35802

AN:

41518

American (AMR)

AF:

0.918

AC:

14030

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.850

AC:

2949

AN:

3468

East Asian (EAS)

AF:

0.640

AC:

3294

AN:

5148

South Asian (SAS)

AF:

0.826

AC:

3984

AN:

4824

European-Finnish (FIN)

AF:

0.855

AC:

9063

AN:

10594

Middle Eastern (MID)

AF:

0.854

AC:

251

AN:

294

European-Non Finnish (NFE)

AF:

0.879

AC:

59762

AN:

68012

Other (OTH)

AF:

0.866

AC:

1824

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

878

1756

2635

3513

4391

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

894

1788

2682

3576

4470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.862

Hom.:

24197

Bravo

AF:

0.871

Asia WGS

AF:

0.771

AC:

2684

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.45

(source)

DANN

Benign

0.50

PhyloP100

-2.2

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over