16-69727830-C-T

Position:

• chr16-69727830-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+655C>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 0.061 in 150,632 control chromosomes in the GnomAD database, including 315 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 0.061 (315 hom., cov: 33)
• Consequence: NQO1-DT ENST00000575838.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NQO1-DT	XR_007065098.1	n.161+655C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NQO1-DT	ENST00000575838.1	n.163+655C>T		intron_variant, non_coding_transcript_variant		5
NQO1-DT	ENST00000690354.1	n.408+655C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0610 AC: 9180 AN: 150514 Hom.: 313 Cov.: 33

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.000776

Gnomad SAS AF: 0.0264

Gnomad FIN AF: 0.0721

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0761

Gnomad OTH AF: 0.0662

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

GnomAD4 genome AF: 0.0610 AC: 9193 AN: 150632 Hom.: 315 Cov.: 33 AF XY: 0.0597 AC XY: 4380 AN XY: 73358

Gnomad4 AFR AF: 0.0446

Gnomad4 AMR AF: 0.0534

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.000778

Gnomad4 SAS AF: 0.0262

Gnomad4 FIN AF: 0.0721

Gnomad4 NFE AF: 0.0762

Gnomad4 OTH AF: 0.0660

Alfa AF: 0.0266 Hom.: 9

Bravo AF: 0.0602

Asia WGS AF: 0.0180 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs689454; hg19: chr16-69761733;