rs17299478

Variant names:

• chr16-69741597-C-T
• rs17299478
• ENST00000575838.2:n.164-538C>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.164-538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,188 control chromosomes in the GnomAD database, including 1,183 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 0.11 (1183 hom., cov: 33)
• Consequence: NQO1-DT ENST00000575838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.33
• Publications: 14 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000575838.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NQO1-DT	NR_186363.1		n.450-538C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NQO1-DT	ENST00000575838.2	TSL:5	n.164-538C>T		intron	N/A
	NQO1-DT	ENST00000844536.1		n.446-530C>T		intron	N/A
	NQO1-DT	ENST00000844537.1		n.162-534C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16942 AN: 152070 Hom.: 1182 Cov.: 33

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.111 AC: 16947 AN: 152188 Hom.: 1183 Cov.: 33 AF XY: 0.109 AC XY: 8135 AN XY: 74404

African (AFR) AF: 0.0279 AC: 1159 AN: 41534

American (AMR) AF: 0.130 AC: 1975 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3470

East Asian (EAS) AF: 0.0782 AC: 406 AN: 5190

South Asian (SAS) AF: 0.122 AC: 590 AN: 4828

European-Finnish (FIN) AF: 0.150 AC: 1594 AN: 10594

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10472 AN: 68004

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.136 Hom.: 2062

Bravo AF: 0.107

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.98
DANN	Benign	0.82
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs17299478; hg19: chr16-69775500;