16-69730509-C-T

Variant summary

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

The ENST00000575838.1(NQO1-DT):n.163+3334C>T variant causes a intron, non coding transcript 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 ENST00000575838.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NQO1-DT	XR_007065098.1	n.162-910C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NQO1-DT	ENST00000575838.1	n.163+3334C>T		intron_variant, non_coding_transcript_variant		5
NQO1-DT	ENST00000690354.1	n.409-910C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.476

Alfa AF: 0.556 Hom.: 24911

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1469908; hg19: chr16-69764412;