16-69727660-C-T

Position:

• chr16-69727660-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+485C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,160 control chromosomes in the GnomAD database, including 57,261 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 0.87 (57261 hom., cov: 31)
• Consequence: NQO1-DT NR_186363.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

Genes affected

NQO1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NQO1-DT	NR_186363.1	n.449+485C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NQO1-DT	ENST00000575838.1	n.163+485C>T		intron_variant		5
NQO1-DT	ENST00000690354.1	n.408+485C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131666 AN: 152042 Hom.: 57218 Cov.: 31

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.866 AC: 131762 AN: 152160 Hom.: 57261 Cov.: 31 AF XY: 0.863 AC XY: 64194 AN XY: 74380

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.918

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.866

Alfa AF: 0.873 Hom.: 9887

Bravo AF: 0.871

Asia WGS AF: 0.771 AC: 2684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs689456; hg19: chr16-69761563;