rs689455

Positions:

• chr16-69727758-T-G

Variant summary

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

The ENST00000575838.1(NQO1-DT):​n.163+583T>G 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 0.217 in 152,104 control chromosomes in the GnomAD database, including 3,914 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 0.22 (3914 hom., cov: 32)
• Consequence: NQO1-DT ENST00000575838.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NQO1-DT	XR_007065098.1	n.161+583T>G		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+583T>G		intron_variant, non_coding_transcript_variant		5
NQO1-DT	ENST00000690354.1	n.408+583T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33004 AN: 151986 Hom.: 3907 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.217 AC: 33036 AN: 152104 Hom.: 3914 Cov.: 32 AF XY: 0.223 AC XY: 16607 AN XY: 74336

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.237

Alfa AF: 0.201 Hom.: 439

Bravo AF: 0.228

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs689455; hg19: chr16-69761661;