chr16-69732388-C-T

Variant summary

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

The ENST00000575838.2(NQO1-DT):​n.163+5213C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,006 control chromosomes in the GnomAD database, including 55,874 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 0.86 ( 55874 hom., cov: 29)

Consequence

NQO1-DT
ENST00000575838.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.95

Publications

10 publications found
Variant links:
Genes affected
NQO1-DT (HGNC:55344): (NQO1 divergent transcript)

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=-1.02).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NQO1-DTNR_186363.1 linkn.449+5213C>T intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NQO1-DTENST00000575838.2 linkn.163+5213C>T intron_variant Intron 1 of 1 5
NQO1-DTENST00000844536.1 linkn.445+5213C>T intron_variant Intron 1 of 1
NQO1-DTENST00000844537.1 linkn.161+5213C>T intron_variant Intron 1 of 1
NQO1-DTENST00000844538.1 linkn.546+11C>T intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.856
AC:
130005
AN:
151888
Hom.:
55833
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.862
Gnomad AMI
AF:
0.878
Gnomad AMR
AF:
0.902
Gnomad ASJ
AF:
0.840
Gnomad EAS
AF:
0.637
Gnomad SAS
AF:
0.826
Gnomad FIN
AF:
0.849
Gnomad MID
AF:
0.851
Gnomad NFE
AF:
0.862
Gnomad OTH
AF:
0.858
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.856
AC:
130099
AN:
152006
Hom.:
55874
Cov.:
29
AF XY:
0.854
AC XY:
63449
AN XY:
74316
show subpopulations
African (AFR)
AF:
0.862
AC:
35728
AN:
41452
American (AMR)
AF:
0.902
AC:
13736
AN:
15234
Ashkenazi Jewish (ASJ)
AF:
0.840
AC:
2916
AN:
3470
East Asian (EAS)
AF:
0.637
AC:
3275
AN:
5144
South Asian (SAS)
AF:
0.826
AC:
3975
AN:
4810
European-Finnish (FIN)
AF:
0.849
AC:
8987
AN:
10586
Middle Eastern (MID)
AF:
0.844
AC:
248
AN:
294
European-Non Finnish (NFE)
AF:
0.862
AC:
58625
AN:
67992
Other (OTH)
AF:
0.856
AC:
1810
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
914
1828
2742
3656
4570
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
892
1784
2676
3568
4460
<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:
0.861
Hom.:
94132
Bravo
AF:
0.859
Asia WGS
AF:
0.767
AC:
2672
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.23
DANN
Benign
0.18
PhyloP100
-1.9

Splicing

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

Publications

Other links and lift over

dbSNP: rs2917682; hg19: chr16-69766291; API