16-69732388-C-T

Position:

• chr16-69732388-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_186363.1(NQO1-DT):​n.449+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 NR_186363.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

NQO1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
NQO1-DT	NR_186363.1	n.449+5213C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NQO1-DT	ENST00000575838.1	n.163+5213C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.856

Alfa AF: 0.859 Hom.: 75235

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2917682; hg19: chr16-69766291;