ENST00000575838.2:n.163+5213C>T

Variant names:

• chr16-69732388-C-T
• rs2917682
• ENST00000575838.2:n.163+5213C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 10 publications found

Genes affected

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

ACMG classification

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-DT	NR_186363.1	n.449+5213C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NQO1-DT	ENST00000575838.2	n.163+5213C>T		intron_variant	Intron 1 of 1	5
NQO1-DT	ENST00000844536.1	n.445+5213C>T		intron_variant	Intron 1 of 1
NQO1-DT	ENST00000844537.1	n.161+5213C>T		intron_variant	Intron 1 of 1
NQO1-DT	ENST00000844538.1	n.546+11C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130005 AN: 151888 Hom.: 55833 Cov.: 29

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

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

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

Other links and lift over

dbSNP: rs2917682; hg19: chr16-69766291;