dbSNP rs689457: NQO1-DT:n.163+98C>T (chr16-69727273-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+98C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0761 in 152,224 control chromosomes in the GnomAD database, including 635 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 0.076 ( 634 hom., cov: 32)

Exomes 𝑓: 0.13 ( 1 hom. )

Consequence

NQO1-DT
ENST00000575838.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Publications

9 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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 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+98C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NQO1-DT	ENST00000575838.2 link	n.163+98C>T	intron_variant	Intron 1 of 1	5
NQO1-DT	ENST00000690354.2 link	n.565+98C>T	intron_variant	Intron 1 of 1
NQO1-DT	ENST00000844536.1 link	n.445+98C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0762

AC:

11585

AN:

152020

Hom.:

634

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0188

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.0702

Gnomad ASJ

AF:

0.0908

Gnomad EAS

AF:

0.000775

Gnomad SAS

AF:

0.0340

Gnomad FIN

AF:

0.176

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.0765

GnomAD4 exome

AF:

0.128

AC:

AN:

Hom.:

AF XY:

0.106

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.111

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0761

AC:

11579

AN:

152138

Hom.:

634

Cov.:

AF XY:

0.0782

AC XY:

5818

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.0187

AC:

778

AN:

41532

American (AMR)

AF:

0.0701

AC:

1071

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0908

AC:

315

AN:

3470

East Asian (EAS)

AF:

0.000777

AC:

AN:

5148

South Asian (SAS)

AF:

0.0344

AC:

166

AN:

4824

European-Finnish (FIN)

AF:

0.176

AC:

1859

AN:

10582

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.106

AC:

7176

AN:

67976

Other (OTH)

AF:

0.0752

AC:

159

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

529

1057

1586

2114

2643

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

130

260

390

520

650

<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:

0.0975

Hom.:

578

Bravo

AF:

0.0662

Asia WGS

AF:

0.0210

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.50

PhyloP100

-0.0070

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over