chr16-69730509-C-T

Variant names:

• chr16-69730509-C-T
• rs1469908
• ENST00000575838.2:n.163+3334C>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+3334C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,044 control chromosomes in the GnomAD database, including 18,322 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 0.47 (18322 hom., cov: 32)
• Consequence: NQO1-DT ENST00000575838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 21 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NQO1-DT	NR_186363.1	n.449+3334C>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+3334C>T		intron_variant	Intron 1 of 1	5
NQO1-DT	ENST00000690354.2	n.566-910C>T		intron_variant	Intron 1 of 1
NQO1-DT	ENST00000844536.1	n.445+3334C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71051 AN: 151926 Hom.: 18330 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.467 AC: 71051 AN: 152044 Hom.: 18322 Cov.: 32 AF XY: 0.464 AC XY: 34472 AN XY: 74326

African (AFR) AF: 0.267 AC: 11063 AN: 41484

American (AMR) AF: 0.472 AC: 7204 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1930 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1055 AN: 5178

South Asian (SAS) AF: 0.458 AC: 2213 AN: 4828

European-Finnish (FIN) AF: 0.585 AC: 6172 AN: 10544

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39780 AN: 67970

Other (OTH) AF: 0.476 AC: 1007 AN: 2114

Alfa AF: 0.547 Hom.: 35879

Bravo AF: 0.448

Asia WGS AF: 0.380 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.1
DANN	Benign	0.14
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs1469908; hg19: chr16-69764412;